diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index affc833710..7c163578ef 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -52,6 +52,12 @@ repos:
     # Check and update the uv lockfile
   - id: uv-lock
 
+- repo: https://github.com/kynan/nbstripout
+  rev: 0.8.1
+  hooks:
+  - id: nbstripout
+    files: \.ipynb$
+
 - repo: local
 
   hooks:
diff --git a/docs/source/howto/interact.rst b/docs/source/howto/interact.rst
index ab6c8c6d85..7177a06e60 100644
--- a/docs/source/howto/interact.rst
+++ b/docs/source/howto/interact.rst
@@ -163,6 +163,43 @@ It is also possible to run ``verdi`` commands inside the notebook, for example:
    %verdi status
 
 
+Running AiiDA engine processes in notebooks
+-------------------------------------------
+
+AiiDA supports running engine processes (such as calculation functions and work chains) directly in Jupyter notebooks.
+When :meth:`~aiida.manage.configuration.load_profile` is called inside a Jupyter notebook, AiiDA automatically sets up the necessary infrastructure to allow synchronous process execution within the notebook's event loop.
+
+.. important::
+
+    ``load_profile()`` must be called in a **separate cell** before any AiiDA engine processes can be executed.
+    The setup takes effect from the **next cell** after loading the profile.
+
+For example, load the profile in the first cell:
+
+.. code-block:: ipython
+
+    In [1]: from aiida import load_profile
+       ...: load_profile()
+
+Then, in a subsequent cell, you can run engine processes as usual:
+
+.. code-block:: ipython
+
+    In [2]: from aiida.engine import calcfunction
+       ...: from aiida import orm
+       ...:
+       ...: @calcfunction
+       ...: def add(x, y):
+       ...:     return orm.Int(x.value + y.value)
+       ...:
+       ...: result = add(orm.Int(3), orm.Int(4))
+       ...: print(result)
+
+.. warning::
+
+    Attempting to run engine processes in the **same cell** where ``load_profile()`` is called will raise an error.
+    Always ensure the profile is loaded in a separate cell.
+
 
 .. _how-to:interact-restapi:
 
diff --git a/docs/source/tutorials/basic.md b/docs/source/tutorials/basic.md
index e490fa13f7..8c14114cb5 100644
--- a/docs/source/tutorials/basic.md
+++ b/docs/source/tutorials/basic.md
@@ -34,6 +34,10 @@ If you are working on your own machine, note that the tutorial assumes that you
 If this is not the case, consult the {ref}`getting started page<installation>`.
 :::
 
+:::{important}
+If you are running this tutorial in a Jupyter notebook, make sure to call `load_profile()` in a **separate cell** before running any AiiDA engine processes (e.g. calculation functions or work chains).
+:::
+
 :::{tip}
 This tutorial can be downloaded and run as a Jupyter Notebook: {nb-download}`basic.ipynb` {octicon}`download`
 :::
diff --git a/environment.yml b/environment.yml
index 62aa69f83f..11ab953543 100644
--- a/environment.yml
+++ b/environment.yml
@@ -12,15 +12,15 @@ dependencies:
 - circus~=0.19.0
 - click-spinner~=0.1.8
 - click<8.3,>=8.1.0
-- disk-objectstore~=1.4.0
+- disk-objectstore~=1.5.0
 - docstring_parser
 - get-annotations~=0.1
 - python-graphviz~=0.19
-- plumpy~=0.25.0
+- plumpy~=0.26.0
 - ipython>=7.6
 - jedi<0.19
 - jinja2~=3.0
-- kiwipy[rmq]~=0.8.4
+- kiwipy[rmq]~=0.9.0
 - importlib-metadata~=6.0
 - numpy<3,>=1.21
 - paramiko~=3.0
diff --git a/pyproject.toml b/pyproject.toml
index 496737aa11..3b9b312d19 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -35,15 +35,15 @@ dependencies = [
   'circus~=0.19.0',
   'click-spinner~=0.1.8',
   'click>=8.1.0,<8.3',
-  'disk-objectstore~=1.4.0',
+  'disk-objectstore~=1.5.0',
   'docstring-parser',
   'get-annotations~=0.1;python_version<"3.10"',
   'graphviz~=0.19',
-  'plumpy~=0.25.0',
+  'plumpy~=0.26.0',
   'ipython>=7.6',
   'jedi<0.19',
   'jinja2~=3.0',
-  'kiwipy[rmq]~=0.8.4',
+  'kiwipy[rmq]~=0.9.0',
   'importlib-metadata~=6.0',
   'numpy>=1.21,<3',
   'paramiko~=3.0',
@@ -274,6 +274,9 @@ ssh_kerberos = [
 tests = [
   'aiida-core[atomic_tools,rest]',
   'aiida-export-migration-tests==0.9.0',
+  'ipykernel~=6.9',
+  'nbclient~=0.10',
+  'nbformat~=5.10',
   'pg8000~=1.13',
   'pgtest~=1.3,>=1.3.1',
   'pytest~=7.0',
@@ -413,7 +416,6 @@ filterwarnings = [
   'ignore:The `Code` class is deprecated.*:aiida.common.warnings.AiidaDeprecationWarning',
   # https://github.com/aiidateam/plumpy/issues/283
   'ignore:There is no current event loop:DeprecationWarning:plumpy',
-  'ignore:There is no current event loop:DeprecationWarning:nest_asyncio',
   # spglib deprecation
   'ignore:dict interface is deprecated:DeprecationWarning',
   # https://github.com/aiidateam/archive-path/issues/21
diff --git a/src/aiida/engine/processes/functions.py b/src/aiida/engine/processes/functions.py
index 08441cddcc..10840968eb 100644
--- a/src/aiida/engine/processes/functions.py
+++ b/src/aiida/engine/processes/functions.py
@@ -601,7 +601,9 @@ async def run(self) -> 'ExitCode' | None:
         # The remaining inputs have to be keyword arguments.
         kwargs.update(**inputs)
 
-        result = self._func(*args, **kwargs)
+        from plumpy import run_with_portal
+
+        result = await run_with_portal(self._func, *args, **kwargs)
 
         if result is None or isinstance(result, ExitCode):  # type: ignore[redundant-expr]
             return result  # type: ignore[unreachable]
diff --git a/src/aiida/engine/processes/futures.py b/src/aiida/engine/processes/futures.py
index 096c11b277..09a9428aa1 100644
--- a/src/aiida/engine/processes/futures.py
+++ b/src/aiida/engine/processes/futures.py
@@ -12,6 +12,7 @@
 from typing import Optional, Union
 
 import kiwipy
+from plumpy import get_or_create_event_loop
 
 from aiida.orm import Node, load_node
 
@@ -43,7 +44,7 @@ def __init__(
         from .process import ProcessState
 
         # create future in specified event loop
-        loop = loop if loop is not None else asyncio.get_event_loop()
+        loop = loop if loop is not None else get_or_create_event_loop()
         super().__init__(loop=loop)
 
         assert not (poll_interval is None and communicator is None), 'Must poll or have a communicator to use'
diff --git a/src/aiida/engine/processes/process.py b/src/aiida/engine/processes/process.py
index b16bd95826..c83e748f33 100644
--- a/src/aiida/engine/processes/process.py
+++ b/src/aiida/engine/processes/process.py
@@ -40,6 +40,7 @@
 import plumpy.persistence
 import plumpy.processes
 from kiwipy.communications import UnroutableError
+from plumpy import run_until_complete
 from plumpy.process_states import Finished, ProcessState
 from plumpy.processes import ConnectionClosed  # type: ignore[attr-defined]
 from plumpy.processes import Process as PlumpyProcess
@@ -361,7 +362,7 @@ def kill(self, msg_text: str | None = None, force_kill: bool = False) -> Union[b
             coro = self._launch_task(task_kill_job, self.node, self.runner.transport)
             self._cancelling_scheduler_job = asyncio.create_task(coro)
             try:
-                self.loop.run_until_complete(self._cancelling_scheduler_job)
+                run_until_complete(self.loop, self._cancelling_scheduler_job)
             except Exception as exc:
                 self.node.logger.error(f'While cancelling the scheduler job an error was raised: {exc}')
                 return False
diff --git a/src/aiida/engine/processes/workchains/workchain.py b/src/aiida/engine/processes/workchains/workchain.py
index 4b847722a0..bb8ac8e94b 100644
--- a/src/aiida/engine/processes/workchains/workchain.py
+++ b/src/aiida/engine/processes/workchains/workchain.py
@@ -15,6 +15,7 @@
 import logging
 import typing as t
 
+from plumpy import run_with_portal
 from plumpy.persistence import auto_persist
 from plumpy.process_states import Continue, Wait
 from plumpy.processes import ProcessStateMachineMeta
@@ -299,7 +300,7 @@ def _update_process_status(self) -> None:
     @Protect.final
     async def run(self) -> t.Any:
         self._stepper = self.spec().get_outline().create_stepper(self)  # type: ignore[arg-type]
-        return self._do_step()
+        return await run_with_portal(self._do_step)
 
     def _do_step(self) -> t.Any:
         """Execute the next step in the outline and return the result.
diff --git a/src/aiida/engine/runners.py b/src/aiida/engine/runners.py
index b19821b2e7..36d35b1139 100644
--- a/src/aiida/engine/runners.py
+++ b/src/aiida/engine/runners.py
@@ -19,8 +19,9 @@
 from typing import Any, Callable, Dict, NamedTuple, Optional, Tuple, Type, Union
 
 import kiwipy
+from plumpy import run_until_complete
 from plumpy.communications import wrap_communicator
-from plumpy.events import reset_event_loop_policy, set_event_loop_policy
+from plumpy.events import get_or_create_event_loop
 from plumpy.persistence import Persister
 from plumpy.process_comms import RemoteProcessThreadController
 
@@ -81,8 +82,7 @@ def __init__(
             broker_submit and persister is None
         ), 'Must supply a persister if you want to submit using communicator'
 
-        set_event_loop_policy()
-        self._loop = loop if loop is not None else asyncio.get_event_loop()
+        self._loop = loop if loop else get_or_create_event_loop()
         self._poll_interval = poll_interval
         self._broker_submit = broker_submit
         self._transport = transports.TransportQueue(self._loop)
@@ -156,8 +156,9 @@ def stop(self) -> None:
 
     def run_until_complete(self, future: asyncio.Future) -> Any:
         """Run the loop until the future has finished and return the result."""
+
         with utils.loop_scope(self._loop):
-            return self._loop.run_until_complete(future)
+            return run_until_complete(self._loop, future)
 
     def close(self) -> None:
         """Close the runner by stopping the loop."""
@@ -165,7 +166,6 @@ def close(self) -> None:
         self.stop()
         if not self._loop.is_running():
             self._loop.close()
-        reset_event_loop_policy()
         self._closed = True
 
     def instantiate_process(self, process: TYPE_RUN_PROCESS, **inputs):
diff --git a/src/aiida/engine/transports.py b/src/aiida/engine/transports.py
index e71b4ab102..2c19b2489b 100644
--- a/src/aiida/engine/transports.py
+++ b/src/aiida/engine/transports.py
@@ -15,6 +15,8 @@
 import traceback
 from typing import TYPE_CHECKING, AsyncIterator, Awaitable, Dict, Hashable, Optional
 
+from plumpy import get_or_create_event_loop
+
 from aiida.orm import AuthInfo
 
 if TYPE_CHECKING:
@@ -44,8 +46,8 @@ class TransportQueue:
     """
 
     def __init__(self, loop: Optional[asyncio.AbstractEventLoop] = None):
-        """:param loop: An asyncio event, will use `asyncio.get_event_loop()` if not supplied"""
-        self._loop = loop if loop is not None else asyncio.get_event_loop()
+        """:param loop: An asyncio event, will use `get_or_create_event_loop()` if not supplied"""
+        self._loop = loop if loop else get_or_create_event_loop()
         self._transport_requests: Dict[Hashable, TransportRequest] = {}
 
     @property
@@ -67,6 +69,15 @@ async def transport_task(transport_queue, authinfo):
         :param authinfo: The authinfo to be used to get transport
         :return: A future that can be yielded to give the transport
         """
+
+        from plumpy import ensure_portal
+
+        # NOTE: We need to ensure the portal here only because
+        # our scheduler has only a sync interface and _get_jobs_from_scheduler is using that
+        # if we ever provide a fully async scheduler interface then we can remove this here
+        # An issue is opened to reference this https://github.com/aiidateam/aiida-core/issues/7222
+        await ensure_portal()
+
         open_callback_handle = None
         transport_request = self._transport_requests.get(authinfo.pk, None)
 
diff --git a/src/aiida/engine/utils.py b/src/aiida/engine/utils.py
index 5fc4335aa4..b8d7cb312e 100644
--- a/src/aiida/engine/utils.py
+++ b/src/aiida/engine/utils.py
@@ -17,6 +17,8 @@
 from datetime import datetime
 from typing import TYPE_CHECKING, Any, Awaitable, Callable, Iterator, List, Optional, Tuple, Type, Union
 
+from plumpy import get_or_create_event_loop
+
 if TYPE_CHECKING:
     from aiida.orm import ProcessNode
 
@@ -125,10 +127,10 @@ def interruptable_task(
     """Turn the given coroutine into an interruptable task by turning it into an InterruptableFuture and returning it.
 
     :param coro: the coroutine that should be made interruptable with object of InterutableFuture as last paramenter
-    :param loop: the event loop in which to run the coroutine, by default uses asyncio.get_event_loop()
+    :param loop: the event loop in which to run the coroutine, by default uses get_or_create_event_loop()
     :return: an InterruptableFuture
     """
-    loop = loop or asyncio.get_event_loop()
+    loop = loop or get_or_create_event_loop()
     future = InterruptableFuture()
 
     async def execute_coroutine():
@@ -252,7 +254,7 @@ def loop_scope(loop) -> Iterator[None]:
 
     :param loop: The event loop to make current for the duration of the scope
     """
-    current = asyncio.get_event_loop()
+    current = get_or_create_event_loop()
 
     try:
         asyncio.set_event_loop(loop)
diff --git a/src/aiida/manage/manager.py b/src/aiida/manage/manager.py
index 26655a51f6..97a18b656e 100644
--- a/src/aiida/manage/manager.py
+++ b/src/aiida/manage/manager.py
@@ -145,9 +145,58 @@ def load_profile(self, profile: Union[None, str, 'Profile'] = None, allow_switch
         # Check whether a development version is being run. Note that needs to be called after ``configure_logging``
         # because this function relies on the logging being properly configured for the warning to show.
         self.check_version()
+        self._setup_event_loop_in_ipython()
 
         return self._profile
 
+    def _setup_event_loop_in_ipython(self) -> None:
+        """Monkey-patch ``IPythonKernel.do_execute`` to ensure a portal.
+
+        When running inside an environment with an already-running event loop
+        (e.g. a Jupyter notebook kernel), this patches the kernel's
+        ``do_execute`` to open a portal before executing each cell.
+        The portal is opended on whichever asyncio task ipykernel uses for that cell.
+
+        The patch takes effect from the **next cell**.
+        ``load_profile()`` must therefore be called in a separate cell before
+        synchronous process execution.
+
+        This is a no-op if no event loop is running (scripts, CLI, daemon).
+        """
+        import asyncio
+
+        try:
+            asyncio.get_running_loop()
+        except RuntimeError:
+            return  # No running loop — not in Jupyter, nothing to do
+
+        self._patch_kernel_do_execute()
+
+    def _patch_kernel_do_execute(self) -> None:
+        """Patch ``IPythonKernel.do_execute`` to ensure a portal before each cell."""
+        try:
+            from ipykernel.ipkernel import IPythonKernel
+
+            if getattr(IPythonKernel, '_aiida_portal_patched', False):
+                return  # Already patched
+
+            from plumpy import ensure_portal
+
+            _orig_do_execute = IPythonKernel.do_execute
+
+            async def _patched_do_execute(self, code, silent, *args, **kwargs):
+                await ensure_portal()
+                return await _orig_do_execute(self, code, silent, *args, **kwargs)
+
+            IPythonKernel.do_execute = _patched_do_execute  # type: ignore[method-assign]
+            IPythonKernel._aiida_portal_patched = True  # type: ignore[attr-defined]
+            self.logger.debug(
+                'Patched IPythonKernel.do_execute for portal. '
+                'This should occur in a Jupyter kernel, and only once per kernel session.'
+            )
+        except Exception:
+            self.logger.debug('Could not patch IPythonKernel for portal.', exc_info=True)
+
     def reset_profile(self) -> None:
         """Close and reset any associated resources for the current profile."""
         self.reset_broker()
diff --git a/src/aiida/manage/tests/pytest_fixtures.py b/src/aiida/manage/tests/pytest_fixtures.py
index 8af0fe0350..465da49a21 100644
--- a/src/aiida/manage/tests/pytest_fixtures.py
+++ b/src/aiida/manage/tests/pytest_fixtures.py
@@ -409,7 +409,7 @@ def clear_database_before_test_class(aiida_profile):
 @pytest.fixture(scope='function')
 def temporary_event_loop():
     """Create a temporary loop for independent test case"""
-    current = asyncio.get_event_loop()
+    current = plumpy.get_or_create_event_loop()
     loop = asyncio.new_event_loop()
     asyncio.set_event_loop(loop)
     try:
diff --git a/src/aiida/repository/backend/disk_object_store.py b/src/aiida/repository/backend/disk_object_store.py
index 9f9eaafc37..fb4ab2adf5 100644
--- a/src/aiida/repository/backend/disk_object_store.py
+++ b/src/aiida/repository/backend/disk_object_store.py
@@ -114,7 +114,7 @@ def open(self, key: str) -> t.Iterator[t.BinaryIO]:
                 yield t.cast(t.BinaryIO, handle)
 
     def iter_object_streams(self, keys: t.Iterable[str]) -> t.Iterator[t.Tuple[str, t.BinaryIO]]:
-        with self._container.get_objects_stream_and_meta(keys) as triplets:  # type: ignore[arg-type]
+        with self._container.get_objects_stream_and_meta(keys) as triplets:
             for key, stream, _ in triplets:
                 assert stream is not None
                 yield key, stream  # type: ignore[misc]
@@ -199,7 +199,7 @@ def maintain(
                 if not dry_run:
                     with get_progress_reporter()(total=1) as progress:
                         callback = create_callback(progress)
-                        container.pack_all_loose(compress=compress_mode, callback=callback)  # type: ignore[arg-type]
+                        container.pack_all_loose(compress=compress_mode, callback=callback)
 
             if do_repack:
                 files_numb = container.count_objects().packed
@@ -208,7 +208,7 @@ def maintain(
                 if not dry_run:
                     with get_progress_reporter()(total=1) as progress:
                         callback = create_callback(progress)
-                        container.repack(callback=callback)  # type: ignore[arg-type]
+                        container.repack(callback=callback)
 
             if clean_storage:
                 logger.report(f'Cleaning the repository database (with `vacuum={do_vacuum}`) ...')
diff --git a/src/aiida/transports/transport.py b/src/aiida/transports/transport.py
index e60034bf33..5f02c59c8d 100644
--- a/src/aiida/transports/transport.py
+++ b/src/aiida/transports/transport.py
@@ -1883,12 +1883,13 @@ class AsyncTransport(Transport):
     """
 
     def run_command_blocking(self, func, *args, **kwargs):
-        """The event loop must be the one of manager."""
+        """Run an async transport method synchronously."""
+        from plumpy import run_until_complete
 
         from aiida.manage import get_manager
 
-        loop = get_manager().get_runner()
-        return loop.run_until_complete(func(*args, **kwargs))
+        loop = get_manager().get_runner().loop
+        return run_until_complete(loop, func(*args, **kwargs))
 
     def open(self):
         return self.run_command_blocking(self.open_async)
diff --git a/tests/conftest.py b/tests/conftest.py
index b93feaf99f..5ef9f0cd8d 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -55,6 +55,12 @@ class TestDbBackend(Enum):
     PSQL = 'psql'
 
 
+@pytest.fixture(autouse=True)
+def _reset_runner(request):
+    yield
+    get_manager().reset_runner()
+
+
 def pytest_collection_modifyitems(items, config):
     """Automatically generate markers for certain tests.
 
diff --git a/tests/engine/test_manager.py b/tests/engine/test_manager.py
index c4ffdab225..cd538de78a 100644
--- a/tests/engine/test_manager.py
+++ b/tests/engine/test_manager.py
@@ -12,6 +12,7 @@
 import time
 
 import pytest
+from plumpy import get_or_create_event_loop
 
 from aiida.engine.processes.calcjobs.manager import JobManager, JobsList
 from aiida.engine.transports import TransportQueue
@@ -24,7 +25,7 @@ class TestJobManager:
     @pytest.fixture(autouse=True)
     def init_profile(self, aiida_localhost):
         """Initialize the profile."""
-        self.loop = asyncio.get_event_loop()
+        self.loop = get_or_create_event_loop()
         self.transport_queue = TransportQueue(self.loop)
         self.user = User.collection.get_default()
         self.computer = aiida_localhost
@@ -54,7 +55,7 @@ class TestJobsList:
     @pytest.fixture(autouse=True)
     def init_profile(self, aiida_localhost):
         """Initialize the profile."""
-        self.loop = asyncio.get_event_loop()
+        self.loop = get_or_create_event_loop()
         self.transport_queue = TransportQueue(self.loop)
         self.user = User.collection.get_default()
         self.computer = aiida_localhost
diff --git a/tests/engine/test_utils.py b/tests/engine/test_utils.py
index fe18020445..151e0b76db 100644
--- a/tests/engine/test_utils.py
+++ b/tests/engine/test_utils.py
@@ -12,6 +12,7 @@
 import contextlib
 
 import pytest
+from plumpy import get_or_create_event_loop
 
 from aiida import orm
 from aiida.engine import calcfunction, workfunction
@@ -43,7 +44,7 @@ def test_exp_backoff_success():
         """Test that exponential backoff will successfully catch exceptions as long as max_attempts is not exceeded."""
         global ITERATION  # noqa: PLW0603
         ITERATION = 0
-        loop = asyncio.get_event_loop()
+        loop = get_or_create_event_loop()
 
         async def coro():
             """A function that will raise RuntimeError as long as ITERATION is smaller than MAX_ITERATIONS."""
@@ -59,7 +60,7 @@ def test_exp_backoff_max_attempts_exceeded(self):
         """Test that exponential backoff will finally raise if max_attempts is exceeded"""
         global ITERATION  # noqa: PLW0603
         ITERATION = 0
-        loop = asyncio.get_event_loop()
+        loop = get_or_create_event_loop()
 
         def coro():
             """A function that will raise RuntimeError as long as ITERATION is smaller than MAX_ITERATIONS."""
@@ -103,7 +104,7 @@ class TestInterruptable:
 
     def test_normal_future(self):
         """Test interrupt future not being interrupted"""
-        loop = asyncio.get_event_loop()
+        loop = get_or_create_event_loop()
 
         interruptable = InterruptableFuture()
         fut = asyncio.Future()
@@ -117,7 +118,7 @@ async def task():
 
     def test_interrupt(self):
         """Test interrupt future being interrupted"""
-        loop = asyncio.get_event_loop()
+        loop = get_or_create_event_loop()
 
         interruptable = InterruptableFuture()
         loop.call_soon(interruptable.interrupt, RuntimeError('STOP'))
@@ -132,7 +133,7 @@ def test_interrupt(self):
 
     def test_inside_interrupted(self):
         """Test interrupt future being interrupted from inside of coroutine"""
-        loop = asyncio.get_event_loop()
+        loop = get_or_create_event_loop()
 
         interruptable = InterruptableFuture()
         fut = asyncio.Future()
@@ -154,7 +155,7 @@ async def task():
 
     def test_interruptable_future_set(self):
         """Test interrupt future being set before coroutine is done"""
-        loop = asyncio.get_event_loop()
+        loop = get_or_create_event_loop()
 
         interruptable = InterruptableFuture()
 
diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/tests/integration/notebook/__init__.py b/tests/integration/notebook/__init__.py
new file mode 100644
index 0000000000..e69de29bb2
diff --git a/tests/integration/notebook/test_magic_cells.ipynb b/tests/integration/notebook/test_magic_cells.ipynb
new file mode 100644
index 0000000000..0c693bb979
--- /dev/null
+++ b/tests/integration/notebook/test_magic_cells.ipynb
@@ -0,0 +1,120 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Test 2: Magic cells after load_profile\n",
+    "\n",
+    "This tests that `%%bash`, `!echo`, `%who` etc. work after the greenback patch is installed."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "%%bash\n",
+    "echo \"Hello from bash!\"\n",
+    "echo \"This should work fine.\"\n",
+    "date"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from aiida import load_profile\n",
+    "from aiida.storage.sqlite_temp import SqliteTempBackend\n",
+    "\n",
+    "profile = load_profile(\n",
+    "    SqliteTempBackend.create_profile(\n",
+    "        'test-magic',\n",
+    "        options={'warnings.development_version': False, 'runner.poll.interval': 1},\n",
+    "        debug=False,\n",
+    "    ),\n",
+    "    allow_switch=True,\n",
+    ")\n",
+    "print('Profile loaded:', profile)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Shell escape with !"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "!echo \"Shell escape works!\"\n",
+    "!ls -la /tmp | head -3"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Line magic %who"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "x = 42\n",
+    "y = 'hello'\n",
+    "%who"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## Verify greenback portal is still active after all that"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import greenback\n",
+    "\n",
+    "print(f'Portal active: {greenback.has_portal()}')\n",
+    "assert greenback.has_portal(), 'Portal should still be active!'"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/tests/integration/notebook/test_notebook_integration.py b/tests/integration/notebook/test_notebook_integration.py
new file mode 100644
index 0000000000..f8a77e1b9e
--- /dev/null
+++ b/tests/integration/notebook/test_notebook_integration.py
@@ -0,0 +1,62 @@
+"""Tests execution of Jupyter notebooks in a real kernel and verify outcomes."""
+
+from pathlib import Path
+
+import nbformat
+import pytest
+from nbclient import NotebookClient
+from nbclient.exceptions import CellExecutionError
+
+NOTEBOOK_DIR = Path(__file__).parent
+
+
+def _execute_notebook(notebook_name, timeout=120):
+    """Execute a notebook and return the executed notebook object."""
+    path = NOTEBOOK_DIR / notebook_name
+    nb = nbformat.read(path, as_version=4)
+    client = NotebookClient(nb, timeout=timeout, kernel_name='python3')
+    client.execute()
+    return nb
+
+
+def _get_cell_outputs(cell, output_type='stream', name='stdout'):
+    """Extract text from cell outputs of a given type."""
+    texts = []
+    for output in cell.outputs:
+        if output.output_type == output_type and output.get('name') == name:
+            texts.append(output.text)
+    return ''.join(texts)
+
+
+@pytest.mark.timeout(180)
+def test_same_cell_fails_with_expected_error():
+    """Test that load_profile + engine call in the same cell fails with a clear error."""
+    path = NOTEBOOK_DIR / 'test_same_cell.ipynb'
+    nb = nbformat.read(path, as_version=4)
+    client = NotebookClient(nb, timeout=120, kernel_name='python3')
+
+    with pytest.raises(CellExecutionError) as exc_info:
+        client.execute()
+
+    code_cell = nb.cells[1]  # Cell index 1, after the markdown cell
+    stdout = _get_cell_outputs(code_cell)
+    assert 'Profile loaded' in stdout
+
+    error_message = str(exc_info.value)
+    # Note: this error message is from plumpy and is not ideal,
+    # but we have to ensure it contains the key information about the nature of the error and how to fix it.
+    assert 'RuntimeError' in error_message
+    assert 'event loop is running but no greenback portal' in error_message
+    assert 'If running in a Jupyter notebook, call load_profile() in a prior cell' in error_message
+
+
+@pytest.mark.timeout(180)
+def test_separate_cell_passes():
+    """Test that load_profile in one cell and engine call in the next cell works."""
+    _execute_notebook('test_separate_cell.ipynb')
+
+
+@pytest.mark.timeout(180)
+def test_magic_cells_passes():
+    """Test that magic commands work correctly after greenback portal is installed."""
+    _execute_notebook('test_magic_cells.ipynb')
diff --git a/tests/integration/notebook/test_same_cell.ipynb b/tests/integration/notebook/test_same_cell.ipynb
new file mode 100644
index 0000000000..d977e872d6
--- /dev/null
+++ b/tests/integration/notebook/test_same_cell.ipynb
@@ -0,0 +1,77 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Test 1: load_profile + multiply in separate cells\n",
+    "\n",
+    "Tests that `load_profile()` in the same cell while having an engine call in the same cells, raises a proper explanation."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from aiida import engine, load_profile, orm\n",
+    "from aiida.storage.sqlite_temp import SqliteTempBackend\n",
+    "\n",
+    "profile = load_profile(\n",
+    "    SqliteTempBackend.create_profile(\n",
+    "        'test-same-cell',\n",
+    "        options={'warnings.development_version': False, 'runner.poll.interval': 1},\n",
+    "        debug=False,\n",
+    "    ),\n",
+    "    allow_switch=True,\n",
+    ")\n",
+    "print('Profile loaded')\n",
+    "\n",
+    "\n",
+    "@engine.calcfunction\n",
+    "def multiply(x, y):\n",
+    "    return x * y\n",
+    "\n",
+    "\n",
+    "# This should fail because load_profile() was not called in a separate cell:\n",
+    "result = multiply(orm.Int(3), orm.Int(4))\n",
+    "print(f'3 * 4 = {result}')\n",
+    "assert result == 12, f'Expected 12, got {result}'\n",
+    "\n",
+    "# Verify it also works for subsequent calls\n",
+    "result2 = multiply(orm.Int(5), orm.Int(6))\n",
+    "print(f'5 * 6 = {result2}')\n",
+    "assert result2 == 30"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/tests/integration/notebook/test_separate_cell.ipynb b/tests/integration/notebook/test_separate_cell.ipynb
new file mode 100644
index 0000000000..055b46b04b
--- /dev/null
+++ b/tests/integration/notebook/test_separate_cell.ipynb
@@ -0,0 +1,77 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Test 1: load_profile + multiply in separate cells\n",
+    "\n",
+    "Tests that `load_profile()` in one cell enables synchronous `multiply(x, y)` in subsequent cells.\n",
+    "Note: `load_profile()` must be in a **separate cell** — same-cell is not supported."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from aiida import engine, load_profile, orm\n",
+    "from aiida.storage.sqlite_temp import SqliteTempBackend\n",
+    "\n",
+    "profile = load_profile(\n",
+    "    SqliteTempBackend.create_profile(\n",
+    "        'test-same-cell',\n",
+    "        options={'warnings.development_version': False, 'runner.poll.interval': 1},\n",
+    "        debug=False,\n",
+    "    ),\n",
+    "    allow_switch=True,\n",
+    ")\n",
+    "print('Profile loaded')"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "@engine.calcfunction\n",
+    "def multiply(x, y):\n",
+    "    return x * y\n",
+    "\n",
+    "\n",
+    "# This works because load_profile() was called in a separate cell:\n",
+    "result = multiply(orm.Int(3), orm.Int(4))\n",
+    "print(f'3 * 4 = {result}')\n",
+    "assert result == 12, f'Expected 12, got {result}'\n",
+    "\n",
+    "# Verify it also works for subsequent calls\n",
+    "result2 = multiply(orm.Int(5), orm.Int(6))\n",
+    "print(f'5 * 6 = {result2}')\n",
+    "assert result2 == 30"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 4
+}
diff --git a/tests/manage/test_manager.py b/tests/manage/test_manager.py
index 3a8f4949cf..08b66cae2f 100644
--- a/tests/manage/test_manager.py
+++ b/tests/manage/test_manager.py
@@ -32,3 +32,15 @@ def test_disconnect():
     assert node.is_finished_ok
     assert result == 2
     manager.reset_profile()  # This hangs before timing out
+
+
+def test_kernel_patch_not_applied_outside_notebook():
+    """Test that ``_setup_event_loop_in_ipython`` does not patch when no event loop is running."""
+    from ipykernel.ipkernel import IPythonKernel
+
+    from aiida.manage.manager import Manager
+
+    manager = Manager()
+    manager._setup_event_loop_in_ipython()
+
+    assert not getattr(IPythonKernel, '_aiida_portal_patched', False)
diff --git a/tests/utils/memory.py b/tests/utils/memory.py
index 1d688740ea..2d0adc151c 100644
--- a/tests/utils/memory.py
+++ b/tests/utils/memory.py
@@ -10,6 +10,7 @@
 
 import asyncio
 
+from plumpy import get_or_create_event_loop
 from pympler import muppy
 
 
@@ -25,7 +26,7 @@ def get_instances(classes, delay=0.0):
         carry, although they may not actually be leaking memory.
     """
     if delay > 0:
-        loop = asyncio.get_event_loop()
+        loop = get_or_create_event_loop()
         loop.run_until_complete(asyncio.sleep(delay))
 
     all_objects = muppy.get_objects()  # this also calls gc.collect()
diff --git a/uv.lock b/uv.lock
index ff82b1d777..223a2b0adb 100644
--- a/uv.lock
+++ b/uv.lock
@@ -107,9 +107,12 @@ pre-commit = [
     { name = "flask" },
     { name = "flask-cors" },
     { name = "flask-restful" },
+    { name = "ipykernel" },
     { name = "matplotlib", version = "3.9.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
     { name = "matplotlib", version = "3.10.7", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" },
     { name = "mypy" },
+    { name = "nbclient" },
+    { name = "nbformat" },
     { name = "packaging" },
     { name = "pg8000" },
     { name = "pgtest" },
@@ -163,8 +166,11 @@ tests = [
     { name = "flask" },
     { name = "flask-cors" },
     { name = "flask-restful" },
+    { name = "ipykernel" },
     { name = "matplotlib", version = "3.9.4", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
     { name = "matplotlib", version = "3.10.7", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" },
+    { name = "nbclient" },
+    { name = "nbformat" },
     { name = "pg8000" },
     { name = "pgtest" },
     { name = "pycifrw" },
@@ -209,7 +215,7 @@ requires-dist = [
     { name = "circus", specifier = "~=0.19.0" },
     { name = "click", specifier = ">=8.1.0,<8.3" },
     { name = "click-spinner", specifier = "~=0.1.8" },
-    { name = "disk-objectstore", specifier = "~=1.4.0" },
+    { name = "disk-objectstore", specifier = "~=1.5.0" },
     { name = "docstring-parser" },
     { name = "docutils", marker = "extra == 'tests'", specifier = "~=0.20" },
     { name = "flask", marker = "extra == 'rest'", specifier = "~=2.3.3" },
@@ -219,15 +225,18 @@ requires-dist = [
     { name = "graphviz", specifier = "~=0.19" },
     { name = "gssapi", marker = "extra == 'ssh-kerberos'", specifier = "~=1.6" },
     { name = "importlib-metadata", specifier = "~=6.0" },
+    { name = "ipykernel", marker = "extra == 'tests'", specifier = "~=6.9" },
     { name = "ipython", specifier = ">=7.6" },
     { name = "jedi", specifier = "<0.19" },
     { name = "jinja2", specifier = "~=3.0" },
     { name = "jupyter", marker = "extra == 'notebook'", specifier = "~=1.0" },
     { name = "jupyter-client", marker = "extra == 'notebook'", specifier = "~=8.0" },
-    { name = "kiwipy", extras = ["rmq"], specifier = "~=0.8.4" },
+    { name = "kiwipy", extras = ["rmq"], specifier = "~=0.9.0" },
     { name = "matplotlib", marker = "extra == 'atomic-tools'", specifier = "~=3.3,>=3.3.4" },
     { name = "mypy", marker = "extra == 'pre-commit'", specifier = "~=1.19.0" },
     { name = "myst-nb", marker = "extra == 'docs'", specifier = "~=1.0.0" },
+    { name = "nbclient", marker = "extra == 'tests'", specifier = "~=0.10" },
+    { name = "nbformat", marker = "extra == 'tests'", specifier = "~=5.10" },
     { name = "notebook", marker = "extra == 'notebook'", specifier = "~=6.1,>=6.1.5" },
     { name = "numpy", specifier = ">=1.21,<3" },
     { name = "packaging", marker = "extra == 'pre-commit'", specifier = "~=23.0" },
@@ -235,7 +244,7 @@ requires-dist = [
     { name = "pg8000", marker = "extra == 'tests'", specifier = "~=1.13" },
     { name = "pgsu", specifier = "~=0.3.0" },
     { name = "pgtest", marker = "extra == 'tests'", specifier = "~=1.3,>=1.3.1" },
-    { name = "plumpy", specifier = "~=0.25.0" },
+    { name = "plumpy", specifier = "~=0.26.0" },
     { name = "pre-commit", marker = "extra == 'pre-commit'", specifier = "~=3.5" },
     { name = "psutil", specifier = "~=7.0" },
     { name = "psycopg", extras = ["binary"], specifier = ">=3.0.2,<4" },
@@ -302,15 +311,44 @@ sdist = { url = "https://files.pythonhosted.org/packages/ea/90/1c9c13f2fdfa96602
 
 [[package]]
 name = "aio-pika"
-version = "9.4.3"
+version = "9.5.6"
 source = { registry = "https://pypi.org/simple" }
+resolution-markers = [
+    "python_full_version < '3.10'",
+]
 dependencies = [
-    { name = "aiormq" },
-    { name = "yarl" },
+    { name = "aiormq", marker = "python_full_version < '3.10'" },
+    { name = "exceptiongroup", marker = "python_full_version < '3.10'" },
+    { name = "typing-extensions", marker = "python_full_version < '3.10'" },
+    { name = "yarl", marker = "python_full_version < '3.10'" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/59/52/fe35c898bce5cc8af839ba786b38f7db8932aac48a67ba8ca7de3b074e07/aio_pika-9.5.6.tar.gz", hash = "sha256:5013f429e1235e1ce8df054a821e0eea140ea9afc94a09725b96590ea2dad001", size = 47308, upload-time = "2025-08-05T14:18:35.949Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/ec/fb/c1cfb7cb98ccd2abdc91e170e7ba0e1e3088b6a9d051e4f2899d3249a231/aio_pika-9.5.6-py3-none-any.whl", hash = "sha256:47b532419185cf1105ae18daa45a5052ff98064915c5e080b2433431fe808193", size = 54303, upload-time = "2025-08-05T14:18:34.62Z" },
+]
+
+[[package]]
+name = "aio-pika"
+version = "9.5.8"
+source = { registry = "https://pypi.org/simple" }
+resolution-markers = [
+    "python_full_version >= '3.14' and sys_platform == 'win32'",
+    "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform == 'win32'",
+    "python_full_version == '3.11.*' and sys_platform == 'win32'",
+    "python_full_version >= '3.14' and sys_platform != 'win32'",
+    "python_full_version >= '3.12' and python_full_version < '3.14' and sys_platform != 'win32'",
+    "python_full_version == '3.11.*' and sys_platform != 'win32'",
+    "python_full_version == '3.10.*' and sys_platform == 'win32'",
+    "python_full_version == '3.10.*' and sys_platform != 'win32'",
+]
+dependencies = [
+    { name = "aiormq", marker = "python_full_version >= '3.10'" },
+    { name = "exceptiongroup", marker = "python_full_version == '3.10.*'" },
+    { name = "yarl", marker = "python_full_version >= '3.10'" },
 ]
-sdist = { url = "https://files.pythonhosted.org/packages/c9/69/8649bdb97fa1521af3dafe23dbc5debadd4b01abb2850a4d193dae9b0451/aio_pika-9.4.3.tar.gz", hash = "sha256:fd2b1fce25f6ed5203ef1dd554dc03b90c9a46a64aaf758d032d78dc31e5295d", size = 47693, upload-time = "2024-08-13T06:49:09.619Z" }
+sdist = { url = "https://files.pythonhosted.org/packages/c5/73/8d1020683970de5532b3b01732d75c8bf922a6505fcdad1a9c7c6405242a/aio_pika-9.5.8.tar.gz", hash = "sha256:7c36874115f522bbe7486c46d8dd711a4dbedd67c4e8a8c47efe593d01862c62", size = 47408, upload-time = "2025-11-12T10:37:10.215Z" }
 wheels = [
-    { url = "https://files.pythonhosted.org/packages/85/66/cad391d83b7266a667c85c826bb6c0d7f68519a0eed7634098c12fb39a4b/aio_pika-9.4.3-py3-none-any.whl", hash = "sha256:f1423d2d5a8b7315d144efe1773763bf687ac17aa1535385982687e9e5ed49bb", size = 53240, upload-time = "2024-08-13T06:49:07.276Z" },
+    { url = "https://files.pythonhosted.org/packages/7c/91/513971861d845d28160ecb205ae2cfaf618b16918a9cd4e0b832b5360ce7/aio_pika-9.5.8-py3-none-any.whl", hash = "sha256:f4c6cb8a6c5176d00f39fd7431e9702e638449bc6e86d1769ad7548b2a506a8d", size = 54397, upload-time = "2025-11-12T10:37:08.374Z" },
 ]
 
 [[package]]
@@ -1867,16 +1905,16 @@ wheels = [
 
 [[package]]
 name = "disk-objectstore"
-version = "1.4.0"
+version = "1.5.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
     { name = "click", version = "8.1.8", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version < '3.10'" },
     { name = "click", version = "8.2.1", source = { registry = "https://pypi.org/simple" }, marker = "python_full_version >= '3.10'" },
     { name = "sqlalchemy" },
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