diff --git a/qlty-check/src/executor.rs b/qlty-check/src/executor.rs
index c1307bf51..9bc947608 100644
--- a/qlty-check/src/executor.rs
+++ b/qlty-check/src/executor.rs
@@ -314,7 +314,20 @@ impl Executor {
 
         let mut loaded_config_files = vec![];
 
-        // load exported config paths before anything else
+        // load repository config files first so that workspace files take
+        // precedence over exported configs in the staging area
+        for config_file in &repository_config_files {
+            if let Err(err) = load_config_file_from_repository(
+                config_file,
+                &self.plan.workspace,
+                &self.plan.staging_area.destination_directory,
+            ) {
+                error!("Failed to load config file from repository: {:?}", err);
+            }
+        }
+
+        // load exported config paths — these are skipped if the file already
+        // exists in the destination (e.g. from a workspace config file above)
         for config_file in &exported_config_paths {
             if self.plan.workspace.root != self.plan.staging_area.destination_directory {
                 // for formatters
@@ -337,16 +350,6 @@ impl Executor {
         self.check_and_copy_configs_into_tool_install(&mut loaded_config_files)?;
         self.plan_plugins_fetch(&mut loaded_config_files)?;
 
-        for config_file in &repository_config_files {
-            if let Err(err) = load_config_file_from_repository(
-                config_file,
-                &self.plan.workspace,
-                &self.plan.staging_area.destination_directory,
-            ) {
-                error!("Failed to load config file from repository: {:?}", err);
-            }
-        }
-
         for config_file in &config_file_names {
             if self.plan.workspace.root != self.plan.staging_area.destination_directory {
                 // for formatters
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/.gitignore b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/.gitignore
new file mode 100644
index 000000000..abbd1c70e
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/.gitignore
@@ -0,0 +1,4 @@
+.qlty/results
+.qlty/logs
+.qlty/out
+.qlty/sources
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/.qlty/qlty.toml b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/.qlty/qlty.toml
new file mode 100644
index 000000000..245a6b2e6
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/.qlty/qlty.toml
@@ -0,0 +1,13 @@
+config_version = "0"
+
+[[source]]
+name = "config-source"
+directory = "config-source"
+
+[[plugin]]
+name = "precedence-linter"
+version = "1.0.0"
+
+[[plugin]]
+name = "precedence-formatter"
+version = "1.0.0"
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/config-source/formatter-results.txt b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/config-source/formatter-results.txt
new file mode 100644
index 000000000..80cc9773a
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/config-source/formatter-results.txt
@@ -0,0 +1 @@
+sample.sh:2:1: EXPORTED formatter used exported config
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/config-source/linter-results.txt b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/config-source/linter-results.txt
new file mode 100644
index 000000000..146f2b5a4
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/config-source/linter-results.txt
@@ -0,0 +1 @@
+sample.sh:2:1: EXPORTED linter used exported config
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/config-source/source.toml b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/config-source/source.toml
new file mode 100644
index 000000000..577a94e0f
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/config-source/source.toml
@@ -0,0 +1,30 @@
+config_version = "0"
+
+[plugins.definitions.precedence-linter]
+file_types = ["shell"]
+config_files = ["linter-results.txt"]
+exported_config_paths = [
+  "linter-results.txt",
+]
+
+[plugins.definitions.precedence-linter.drivers.lint]
+prepare_script = "mkdir ${linter} && echo type %1 > ${linter}/cat.cmd || echo type %1 > ${linter}/cat.cmd"
+script = "cat linter-results.txt"
+output_format = "regex"
+output_regex = "((?P<path>.*):(?P<line>-?\\d+):(?P<col>-?\\d+): (?P<code>\\S+) (?P<message>.+))\n"
+success_codes = [0]
+
+[plugins.definitions.precedence-formatter]
+file_types = ["shell"]
+config_files = ["formatter-results.txt"]
+exported_config_paths = [
+  "formatter-results.txt",
+]
+
+[plugins.definitions.precedence-formatter.drivers.fmt]
+driver_type = "formatter"
+prepare_script = "mkdir ${linter} && echo type %1 > ${linter}/cat.cmd || echo type %1 > ${linter}/cat.cmd"
+script = "cat formatter-results.txt"
+output_format = "regex"
+output_regex = "((?P<path>.*):(?P<line>-?\\d+):(?P<col>-?\\d+): (?P<code>\\S+) (?P<message>.+))\n"
+success_codes = [0]
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/formatter-results.txt b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/formatter-results.txt
new file mode 100644
index 000000000..001cfd4a8
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/formatter-results.txt
@@ -0,0 +1 @@
+sample.sh:2:1: WORKSPACE formatter used workspace config
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/linter-results.txt b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/linter-results.txt
new file mode 100644
index 000000000..d28b6ed77
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/linter-results.txt
@@ -0,0 +1 @@
+sample.sh:2:1: WORKSPACE linter used workspace config
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/sample.sh b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/sample.sh
new file mode 100644
index 000000000..4163036ef
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.in/sample.sh
@@ -0,0 +1,2 @@
+#!/bin/sh
+echo hi
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.stderr b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.stderr
new file mode 100644
index 000000000..eb07d1161
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.stderr
@@ -0,0 +1 @@
+✖ 2 issues
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.stdout b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.stdout
new file mode 100644
index 000000000..c0bc23a5d
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.stdout
@@ -0,0 +1,7 @@
+
+ ISSUES: 2[..]
+
+sample.sh:2:0
+    2:0  medium  formatter used workspace config  precedence-formatter:WORKSPACE[..]
+    2:0  medium  linter used workspace config     precedence-linter:WORKSPACE[..]
+[..]
diff --git a/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.toml b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.toml
new file mode 100644
index 000000000..ca7a5c984
--- /dev/null
+++ b/qlty-cli/tests/cmd/check/exported_config_workspace_precedence.toml
@@ -0,0 +1,3 @@
+bin.name = "qlty"
+args = ["check", "--all", "--no-cache"]
+status.code = 1