diff --git a/lib/analyze-action.js b/lib/analyze-action.js
index d66eb32fd..d15c8977c 100644
--- a/lib/analyze-action.js
+++ b/lib/analyze-action.js
@@ -94197,6 +94197,9 @@ function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
   }
   return augmentedConfig;
 }
+function isCodeScanningEnabled(config) {
+  return config.analysisKinds.includes("code-scanning" /* CodeScanning */);
+}
 function isCodeQualityEnabled(config) {
   return config.analysisKinds.includes("code-quality" /* CodeQuality */);
 }
@@ -96179,7 +96182,7 @@ async function runQueries(sarifFolder, memoryFlag, addSnippetsFlag, threadsFlag,
     try {
       const sarifFile = path12.join(sarifFolder, `${language}.sarif`);
       const queries = [];
-      if (isCodeQualityEnabled(config)) {
+      if (isCodeQualityEnabled(config) && isCodeScanningEnabled(config)) {
         queries.push(getGeneratedSuitePath(config, language));
         for (const qualityQuery of config.augmentationProperties.qualityQueriesInput) {
           queries.push(resolveQuerySuiteAlias(language, qualityQuery.uses));
diff --git a/src/analyze.ts b/src/analyze.ts
index dad12d78c..b597281f9 100644
--- a/src/analyze.ts
+++ b/src/analyze.ts
@@ -661,8 +661,19 @@ export async function runQueries(
     try {
       const sarifFile = path.join(sarifFolder, `${language}.sarif`);
 
+      // This should be empty to run only the query suite that was generated when
+      // the database was initialised.
       const queries: string[] = [];
-      if (configUtils.isCodeQualityEnabled(config)) {
+
+      // If both Code Scanning and Code Quality analyses are enabled, the database
+      // is initialised for Code Scanning. To avoid duplicate work, we want to run
+      // queries for both analyses at the same time. To do this, we invoke `run-queries`
+      // once with the generated query suite for Code Scanning + the fixed
+      // query suite for Code Quality.
+      if (
+        configUtils.isCodeQualityEnabled(config) &&
+        configUtils.isCodeScanningEnabled(config)
+      ) {
         queries.push(util.getGeneratedSuitePath(config, language));
         for (const qualityQuery of config.augmentationProperties
           .qualityQueriesInput) {