diff --git a/.github/workflows/__quality-queries.yml b/.github/workflows/__quality-queries.yml
index 9cb7ee8e7..0da9d80ee 100644
--- a/.github/workflows/__quality-queries.yml
+++ b/.github/workflows/__quality-queries.yml
@@ -67,40 +67,51 @@ jobs:
       - name: Upload security SARIF
         uses: actions/upload-artifact@v4
         with:
-          name: config-export-${{ matrix.os }}-${{ matrix.version }}.sarif.json
+          name: quality-queries-${{ matrix.os }}-${{ matrix.version }}.sarif.json
           path: ${{ runner.temp }}/results/javascript.sarif
           retention-days: 7
       - name: Upload quality SARIF
         uses: actions/upload-artifact@v4
         with:
-          name: config-export-${{ matrix.os }}-${{ matrix.version }}.quality.sarif.json
+          name: quality-queries-${{ matrix.os }}-${{ matrix.version }}.quality.sarif.json
           path: ${{ runner.temp }}/results/javascript.quality.sarif
           retention-days: 7
-      - name: Check config properties appear in SARIF
+      - name: Check quality query does not appear in security SARIF
+        uses: actions/github-script@v7
+        env:
+          SARIF_PATH: ${{ runner.temp }}/results/javascript.sarif
+          EXPECT_PRESENT: 'false'
+        with:
+          script: ${{ env.CHECK_SCRIPT }}
+      - name: Check quality query appears in quality SARIF
         uses: actions/github-script@v7
         env:
           SARIF_PATH: ${{ runner.temp }}/results/javascript.quality.sarif
+          EXPECT_PRESENT: 'true'
         with:
-          script: |
-            const fs = require('fs');
-
-            const sarif = JSON.parse(fs.readFileSync(process.env['SARIF_PATH'], 'utf8'));
-            const run = sarif.runs[0];
-            const configSummary = run.properties.codeqlConfigSummary;
-
-            if (configSummary === undefined) {
-              core.setFailed('`codeqlConfigSummary` property not found in the SARIF run property bag.');
-            }
-            if (configSummary.disableDefaultQueries !== false) {
-              core.setFailed('`disableDefaultQueries` property incorrect: expected false, got ' +
-                `${JSON.stringify(configSummary.disableDefaultQueries)}.`);
-            }
-            const expectedQueries = [{ type: 'builtinSuite', uses: 'code-quality' }];
-            // Use JSON.stringify to deep-equal the arrays.
-            if (JSON.stringify(configSummary.queries) !== JSON.stringify(expectedQueries)) {
-              core.setFailed(`\`queries\` property incorrect: expected ${JSON.stringify(expectedQueries)}, got ` +
-                `${JSON.stringify(configSummary.queries)}.`);
-            }
-            core.info('Finished config export tests.');
+          script: ${{ env.CHECK_SCRIPT }}
     env:
+      CHECK_SCRIPT: |
+        const fs = require('fs');
+
+        const sarif = JSON.parse(fs.readFileSync(process.env['SARIF_PATH'], 'utf8'));
+        const expectPresent = JSON.parse(process.env['EXPECT_PRESENT']);
+        const run = sarif.runs[0];
+        const extensions = run.tool.extensions;
+
+        if (extensions === undefined) {
+          core.setFailed('`extensions` property not found in the SARIF run property bag.');
+        }
+
+        // ID of a query we want to check the presence for
+        const targetId = 'js/regex/always-matches';
+        const found = extensions.find(extension => extension.rules && extension.rules.find(rule => rule.id === targetId));
+
+        if (found && expectPresent) {
+          console.log(`Found rule with id '${targetId}'.`);
+        } else if (!found && !expectPresent) {
+          console.log(`Rule with id '${targetId}' was not found.`);
+        } else {
+          core.setFailed(`${ found ? "Found" : "Didn't find" } rule ${targetId}`);
+        }
       CODEQL_ACTION_TEST_MODE: true
diff --git a/pr-checks/checks/quality-queries.yml b/pr-checks/checks/quality-queries.yml
index a15d8a3ac..6cf07e247 100644
--- a/pr-checks/checks/quality-queries.yml
+++ b/pr-checks/checks/quality-queries.yml
@@ -1,6 +1,30 @@
 name: "Quality queries input"
 description: "Tests that queries specified in the quality-queries input are used."
 versions: ["linked", "nightly-latest"]
+env:
+  CHECK_SCRIPT: |
+    const fs = require('fs');
+
+    const sarif = JSON.parse(fs.readFileSync(process.env['SARIF_PATH'], 'utf8'));
+    const expectPresent = JSON.parse(process.env['EXPECT_PRESENT']);
+    const run = sarif.runs[0];
+    const extensions = run.tool.extensions;
+
+    if (extensions === undefined) {
+      core.setFailed('`extensions` property not found in the SARIF run property bag.');
+    }
+
+    // ID of a query we want to check the presence for
+    const targetId = 'js/regex/always-matches';
+    const found = extensions.find(extension => extension.rules && extension.rules.find(rule => rule.id === targetId));
+
+    if (found && expectPresent) {
+      console.log(`Found rule with id '${targetId}'.`);
+    } else if (!found && !expectPresent) {
+      console.log(`Rule with id '${targetId}' was not found.`);
+    } else {
+      core.setFailed(`${ found ? "Found" : "Didn't find" } rule ${targetId}`);
+    }
 steps:
   - uses: ./../action/init
     with:
@@ -14,38 +38,26 @@ steps:
   - name: Upload security SARIF
     uses: actions/upload-artifact@v4
     with:
-      name: config-export-${{ matrix.os }}-${{ matrix.version }}.sarif.json
+      name: quality-queries-${{ matrix.os }}-${{ matrix.version }}.sarif.json
       path: "${{ runner.temp }}/results/javascript.sarif"
       retention-days: 7
   - name: Upload quality SARIF
     uses: actions/upload-artifact@v4
     with:
-      name: config-export-${{ matrix.os }}-${{ matrix.version }}.quality.sarif.json
+      name: quality-queries-${{ matrix.os }}-${{ matrix.version }}.quality.sarif.json
       path: "${{ runner.temp }}/results/javascript.quality.sarif"
       retention-days: 7
-  - name: Check config properties appear in SARIF
+  - name: Check quality query does not appear in security SARIF
+    uses: actions/github-script@v7
+    env:
+      SARIF_PATH: "${{ runner.temp }}/results/javascript.sarif"
+      EXPECT_PRESENT: "false"
+    with:
+      script: ${{ env.CHECK_SCRIPT }}
+  - name: Check quality query appears in quality SARIF
     uses: actions/github-script@v7
     env:
       SARIF_PATH: "${{ runner.temp }}/results/javascript.quality.sarif"
+      EXPECT_PRESENT: "true"
     with:
-      script: |
-        const fs = require('fs');
-
-        const sarif = JSON.parse(fs.readFileSync(process.env['SARIF_PATH'], 'utf8'));
-        const run = sarif.runs[0];
-        const configSummary = run.properties.codeqlConfigSummary;
-
-        if (configSummary === undefined) {
-          core.setFailed('`codeqlConfigSummary` property not found in the SARIF run property bag.');
-        }
-        if (configSummary.disableDefaultQueries !== false) {
-          core.setFailed('`disableDefaultQueries` property incorrect: expected false, got ' +
-            `${JSON.stringify(configSummary.disableDefaultQueries)}.`);
-        }
-        const expectedQueries = [{ type: 'builtinSuite', uses: 'code-quality' }];
-        // Use JSON.stringify to deep-equal the arrays.
-        if (JSON.stringify(configSummary.queries) !== JSON.stringify(expectedQueries)) {
-          core.setFailed(`\`queries\` property incorrect: expected ${JSON.stringify(expectedQueries)}, got ` +
-            `${JSON.stringify(configSummary.queries)}.`);
-        }
-        core.info('Finished config export tests.');
+      script: ${{ env.CHECK_SCRIPT }}