diff --git a/.github/workflows/__quality-queries.yml b/.github/workflows/__quality-queries.yml
index 1578d4c7a..8b74c1c7f 100644
--- a/.github/workflows/__quality-queries.yml
+++ b/.github/workflows/__quality-queries.yml
@@ -32,16 +32,58 @@ jobs:
         include:
           - os: ubuntu-latest
             version: linked
+            analysis-kinds: code-scanning
+          - os: ubuntu-latest
+            version: linked
+            analysis-kinds: code-quality
+          - os: ubuntu-latest
+            version: linked
+            analysis-kinds: code-scanning,code-quality
           - os: macos-latest
             version: linked
+            analysis-kinds: code-scanning
+          - os: macos-latest
+            version: linked
+            analysis-kinds: code-quality
+          - os: macos-latest
+            version: linked
+            analysis-kinds: code-scanning,code-quality
           - os: windows-latest
             version: linked
+            analysis-kinds: code-scanning
+          - os: windows-latest
+            version: linked
+            analysis-kinds: code-quality
+          - os: windows-latest
+            version: linked
+            analysis-kinds: code-scanning,code-quality
           - os: ubuntu-latest
             version: nightly-latest
+            analysis-kinds: code-scanning
+          - os: ubuntu-latest
+            version: nightly-latest
+            analysis-kinds: code-quality
+          - os: ubuntu-latest
+            version: nightly-latest
+            analysis-kinds: code-scanning,code-quality
           - os: macos-latest
             version: nightly-latest
+            analysis-kinds: code-scanning
+          - os: macos-latest
+            version: nightly-latest
+            analysis-kinds: code-quality
+          - os: macos-latest
+            version: nightly-latest
+            analysis-kinds: code-scanning,code-quality
           - os: windows-latest
             version: nightly-latest
+            analysis-kinds: code-scanning
+          - os: windows-latest
+            version: nightly-latest
+            analysis-kinds: code-quality
+          - os: windows-latest
+            version: nightly-latest
+            analysis-kinds: code-scanning,code-quality
     name: Quality queries input
     permissions:
       contents: read
@@ -61,25 +103,28 @@ jobs:
       - uses: ./../action/init
         with:
           languages: javascript
-          analysis-kinds: code-scanning,code-quality
+          analysis-kinds: ${{ matrix.analysis-kinds }}
           tools: ${{ steps.prepare-test.outputs.tools-url }}
       - uses: ./../action/analyze
         with:
           output: ${{ runner.temp }}/results
           upload-database: false
       - name: Upload security SARIF
+        if: contains(matrix.analysis-kinds, 'code-scanning')
         uses: actions/upload-artifact@v4
         with:
           name: quality-queries-${{ matrix.os }}-${{ matrix.version }}.sarif.json
           path: ${{ runner.temp }}/results/javascript.sarif
           retention-days: 7
       - name: Upload quality SARIF
+        if: contains(matrix.analysis-kinds, 'code-quality')
         uses: actions/upload-artifact@v4
         with:
           name: quality-queries-${{ matrix.os }}-${{ matrix.version }}.quality.sarif.json
           path: ${{ runner.temp }}/results/javascript.quality.sarif
           retention-days: 7
       - name: Check quality query does not appear in security SARIF
+        if: contains(matrix.analysis-kinds, 'code-scanning')
         uses: actions/github-script@v7
         env:
           SARIF_PATH: ${{ runner.temp }}/results/javascript.sarif
@@ -87,6 +132,7 @@ jobs:
         with:
           script: ${{ env.CHECK_SCRIPT }}
       - name: Check quality query appears in quality SARIF
+        if: contains(matrix.analysis-kinds, 'code-quality')
         uses: actions/github-script@v7
         env:
           SARIF_PATH: ${{ runner.temp }}/results/javascript.quality.sarif
diff --git a/pr-checks/checks/quality-queries.yml b/pr-checks/checks/quality-queries.yml
index 3f4ff3b1b..618f8e4cf 100644
--- a/pr-checks/checks/quality-queries.yml
+++ b/pr-checks/checks/quality-queries.yml
@@ -1,6 +1,7 @@
 name: "Quality queries input"
 description: "Tests that queries specified in the quality-queries input are used."
 versions: ["linked", "nightly-latest"]
+analysisKinds: ["code-scanning", "code-quality", "code-scanning,code-quality"]
 env:
   CHECK_SCRIPT: |
     const fs = require('fs');
@@ -29,25 +30,28 @@ steps:
   - uses: ./../action/init
     with:
       languages: javascript
-      analysis-kinds: code-scanning,code-quality
+      analysis-kinds: ${{ matrix.analysis-kinds }}
       tools: ${{ steps.prepare-test.outputs.tools-url }}
   - uses: ./../action/analyze
     with:
       output: "${{ runner.temp }}/results"
       upload-database: false
   - name: Upload security SARIF
+    if: contains(matrix.analysis-kinds, 'code-scanning')
     uses: actions/upload-artifact@v4
     with:
       name: quality-queries-${{ matrix.os }}-${{ matrix.version }}.sarif.json
       path: "${{ runner.temp }}/results/javascript.sarif"
       retention-days: 7
   - name: Upload quality SARIF
+    if: contains(matrix.analysis-kinds, 'code-quality')
     uses: actions/upload-artifact@v4
     with:
       name: quality-queries-${{ matrix.os }}-${{ matrix.version }}.quality.sarif.json
       path: "${{ runner.temp }}/results/javascript.quality.sarif"
       retention-days: 7
   - name: Check quality query does not appear in security SARIF
+    if: contains(matrix.analysis-kinds, 'code-scanning')
     uses: actions/github-script@v7
     env:
       SARIF_PATH: "${{ runner.temp }}/results/javascript.sarif"
@@ -55,6 +59,7 @@ steps:
     with:
       script: ${{ env.CHECK_SCRIPT }}
   - name: Check quality query appears in quality SARIF
+    if: contains(matrix.analysis-kinds, 'code-quality')
     uses: actions/github-script@v7
     env:
       SARIF_PATH: "${{ runner.temp }}/results/javascript.quality.sarif"
diff --git a/pr-checks/sync.py b/pr-checks/sync.py
index beaa94398..6d23cafab 100755
--- a/pr-checks/sync.py
+++ b/pr-checks/sync.py
@@ -102,6 +102,18 @@ for file in sorted((this_dir / 'checks').glob('*.yml')):
         if checkSpecification.get('useAllPlatformBundle'):
             useAllPlatformBundle = checkSpecification['useAllPlatformBundle']
 
+
+    if 'analysisKinds' in checkSpecification:
+        newMatrix = []
+        for matrixInclude in matrix:
+            for analysisKind in checkSpecification.get('analysisKinds'):
+                newMatrix.append(
+                    matrixInclude |
+                    { 'analysis-kinds': analysisKind }
+                )
+        matrix = newMatrix
+
+    # Construct the workflow steps needed for this check.
     steps = [
         {
             'name': 'Check out repository',