diff --git a/lib/pix/command/graph.ex b/lib/pix/command/graph.ex
index 22e726f..61712b8 100644
--- a/lib/pix/command/graph.ex
+++ b/lib/pix/command/graph.ex
@@ -6,7 +6,7 @@ defmodule Pix.Command.Graph do
   @spec cmd(Pix.UserSettings.t(), Pix.Config.t(), OptionParser.argv()) :: :ok
   def cmd(user_settings, config, argv) do
     {cli_opts, args} = Pix.Helper.option_parser_parse!(argv, strict: @cli_args)
-    cli_opts = Keyword.merge(cli_opts, user_settings.command.graph.cli_opts)
+    cli_opts = Keyword.merge(user_settings.command.graph.cli_opts, cli_opts)
     config_pipelines = config.pipelines
 
     case args do
diff --git a/lib/pix/command/ls.ex b/lib/pix/command/ls.ex
index 1fd423e..9590eac 100644
--- a/lib/pix/command/ls.ex
+++ b/lib/pix/command/ls.ex
@@ -6,7 +6,7 @@ defmodule Pix.Command.Ls do
   @spec cmd(Pix.UserSettings.t(), Pix.Config.t(), OptionParser.argv()) :: :ok
   def cmd(user_settings, config, argv) do
     {cli_opts, args} = Pix.Helper.option_parser_parse!(argv, strict: @cli_args)
-    cli_opts = Keyword.merge(cli_opts, user_settings.command.ls.cli_opts)
+    cli_opts = Keyword.merge(user_settings.command.ls.cli_opts, cli_opts)
     verbose? = Keyword.get(cli_opts, :verbose, false)
     hidden? = Keyword.get(cli_opts, :hidden, false)
     config_pipelines = config.pipelines
diff --git a/lib/pix/command/run.ex b/lib/pix/command/run.ex
index 3af4780..1ed5775 100644
--- a/lib/pix/command/run.ex
+++ b/lib/pix/command/run.ex
@@ -17,7 +17,7 @@ defmodule Pix.Command.Run do
   @spec cmd(Pix.UserSettings.t(), Pix.Config.t(), OptionParser.argv()) :: :ok
   def cmd(user_settings, config, argv) do
     {cli_opts, args} = Pix.Helper.option_parser_parse!(argv, strict: @cli_args)
-    cli_opts = Keyword.merge(cli_opts, user_settings.command.run.cli_opts)
+    cli_opts = Keyword.merge(user_settings.command.run.cli_opts, cli_opts)
     config_pipelines = config.pipelines
 
     validate_run_cli_opts!(cli_opts)
diff --git a/lib/pix/command/shell.ex b/lib/pix/command/shell.ex
index 4479c3e..e6ac355 100644
--- a/lib/pix/command/shell.ex
+++ b/lib/pix/command/shell.ex
@@ -12,7 +12,7 @@ defmodule Pix.Command.Shell do
   @spec cmd(Pix.UserSettings.t(), Pix.Config.t(), OptionParser.argv()) :: :ok
   def cmd(user_settings, config, argv) do
     {cli_opts, args} = Pix.Helper.option_parser_parse!(argv, strict: @cli_args)
-    cli_opts = Keyword.merge(cli_opts, user_settings.command.shell.cli_opts)
+    cli_opts = Keyword.merge(user_settings.command.shell.cli_opts, cli_opts)
     config_pipelines = config.pipelines
 
     case args do
diff --git a/lib/pix/command/upgrade.ex b/lib/pix/command/upgrade.ex
index 414a529..08df633 100644
--- a/lib/pix/command/upgrade.ex
+++ b/lib/pix/command/upgrade.ex
@@ -9,7 +9,7 @@ defmodule Pix.Command.Upgrade do
   def cmd(user_settings, argv) do
     {cli_opts, _args} = Pix.Helper.option_parser_parse!(argv, strict: @cli_args)
 
-    cli_opts = Keyword.merge(cli_opts, user_settings.command.upgrade.cli_opts)
+    cli_opts = Keyword.merge(user_settings.command.upgrade.cli_opts, cli_opts)
     dry_run? = Keyword.get(cli_opts, :dry_run, false)
 
     current_version = Application.fetch_env!(:pix, :version)