diff --git a/lib/setup-codeql.js b/lib/setup-codeql.js
index b451f3074..104af5b2e 100644
--- a/lib/setup-codeql.js
+++ b/lib/setup-codeql.js
@@ -417,16 +417,22 @@ const downloadCodeQL = async function (codeqlURL, maybeBundleVersion, maybeCliVe
             toolsVersion: maybeCliVersion ?? "unknown",
         };
     }
-    logger.debug("Caching CodeQL bundle.");
-    const toolcacheStart = perf_hooks_1.performance.now();
-    const toolcachedBundlePath = await toolcache.cacheDir(extractedBundlePath, "CodeQL", toolcacheInfo.version);
-    logger.info(`Added CodeQL bundle to the tool cache (${(0, logging_1.formatDuration)(perf_hooks_1.performance.now() - toolcacheStart)}).`);
-    // Defensive check: we expect `cacheDir` to copy the bundle to a new location.
-    if (toolcachedBundlePath !== extractedBundlePath) {
-        await (0, util_1.cleanUpGlob)(extractedBundlePath, "CodeQL bundle from temporary directory", logger);
+    let codeqlFolder = extractedBundlePath;
+    if (extractToToolcache) {
+        (0, tools_download_1.writeToolcacheMarkerFile)(toolcacheInfo.path, logger);
+    }
+    else {
+        logger.debug("Caching CodeQL bundle.");
+        const toolcacheStart = perf_hooks_1.performance.now();
+        codeqlFolder = await toolcache.cacheDir(extractedBundlePath, "CodeQL", toolcacheInfo.version);
+        logger.info(`Added CodeQL bundle to the tool cache (${(0, logging_1.formatDuration)(perf_hooks_1.performance.now() - toolcacheStart)}).`);
+        // Defensive check: we expect `cacheDir` to copy the bundle to a new location.
+        if (codeqlFolder !== extractedBundlePath) {
+            await (0, util_1.cleanUpGlob)(extractedBundlePath, "CodeQL bundle from temporary directory", logger);
+        }
     }
     return {
-        codeqlFolder: toolcachedBundlePath,
+        codeqlFolder,
         statusReport,
         toolsVersion: maybeCliVersion ?? toolcacheInfo.version,
     };
diff --git a/lib/setup-codeql.js.map b/lib/setup-codeql.js.map
index 9892a0149..f251d5c1f 100644
--- a/lib/setup-codeql.js.map
+++ b/lib/setup-codeql.js.map
@@ -1 +1 @@
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\ No newline at end of file
diff --git a/lib/tools-download.js b/lib/tools-download.js
index 818cd912b..8b68daea9 100644
--- a/lib/tools-download.js
+++ b/lib/tools-download.js
@@ -26,6 +26,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.STREAMING_HIGH_WATERMARK_BYTES = void 0;
 exports.downloadAndExtract = downloadAndExtract;
 exports.getToolcacheDirectory = getToolcacheDirectory;
+exports.writeToolcacheMarkerFile = writeToolcacheMarkerFile;
+const fs = __importStar(require("fs"));
 const os = __importStar(require("os"));
 const path = __importStar(require("path"));
 const perf_hooks_1 = require("perf_hooks");
@@ -114,6 +116,11 @@ async function downloadAndExtractZstdWithStreaming(codeqlURL, dest, authorizatio
 function getToolcacheDirectory(version) {
     return path.join((0, util_1.getRequiredEnvParam)("RUNNER_TOOL_CACHE"), TOOLCACHE_TOOL_NAME, semver.clean(version) || version, os.arch() || "");
 }
+function writeToolcacheMarkerFile(extractedPath, logger) {
+    const markerFilePath = `${extractedPath}.complete`;
+    fs.writeFileSync(markerFilePath, "");
+    logger.debug(`Wrote marker file to ${markerFilePath}`);
+}
 function sanitizeUrlForStatusReport(url) {
     return ["github/codeql-action", "dsp-testing/codeql-cli-nightlies"].some((repo) => url.startsWith(`https://github.com/${repo}/releases/download/`))
         ? url
diff --git a/lib/tools-download.js.map b/lib/tools-download.js.map
index 42a9e3c44..72649ddf1 100644
--- a/lib/tools-download.js.map
+++ b/lib/tools-download.js.map
@@ -1 +1 @@
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\ No newline at end of file
+{"version":3,"file":"tools-download.js","sourceRoot":"","sources":["../src/tools-download.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;AAgFA,gDA+FC;AAoCD,sDAOC;AAED,4DAOC;AAnOD,uCAAyB;AAEzB,uCAAyB;AACzB,2CAA6B;AAC7B,2CAAyC;AAEzC,+DAAiD;AACjD,uDAAyC;AACzC,+CAAiC;AAEjC,mDAA6D;AAC7D,uCAAmD;AACnD,2CAA6B;AAC7B,iCAA0D;AAE1D;;GAEG;AACU,QAAA,8BAA8B,GAAG,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,CAAC,QAAQ;AAEvE;;GAEG;AACH,MAAM,mBAAmB,GAAG,QAAQ,CAAC;AAarC,SAAS,uCAAuC,CAC9C,kBAA0B,EAC1B,oBAA4B;IAE5B,OAAO;QACL,kBAAkB,EAAE,kBAAkB,GAAG,oBAAoB;QAC7D,kBAAkB;QAClB,oBAAoB;QACpB,gBAAgB,EAAE,KAAK;KACxB,CAAC;AACJ,CAAC;AAaD,SAAS,kCAAkC,CACzC,kBAA0B;IAE1B,OAAO;QACL,kBAAkB;QAClB,kBAAkB,EAAE,SAAS;QAC7B,oBAAoB,EAAE,SAAS;QAC/B,gBAAgB,EAAE,IAAI;KACvB,CAAC;AACJ,CAAC;AAYM,KAAK,UAAU,kBAAkB,CACtC,SAAiB,EACjB,IAAY,EACZ,aAAiC,EACjC,OAA4B,EAC5B,UAAsC,EACtC,QAA2B,EAC3B,MAAc;IAEd,MAAM,CAAC,IAAI,CACT,iCAAiC,SAAS,2BAA2B,CACtE,CAAC;IAEF,MAAM,iBAAiB,GAAG,GAAG,CAAC,sBAAsB,CAAC,SAAS,CAAC,CAAC;IAEhE,wFAAwF;IAExF,IACE,CAAC,MAAM,QAAQ,CAAC,QAAQ,CAAC,uBAAO,CAAC,6BAA6B,CAAC,CAAC;QAChE,iBAAiB,KAAK,MAAM;QAC5B,OAAO,CAAC,QAAQ,KAAK,OAAO,EAC5B,CAAC;QACD,MAAM,CAAC,IAAI,CAAC,gDAAgD,CAAC,CAAC;QAE9D,MAAM,iBAAiB,GAAG,wBAAW,CAAC,GAAG,EAAE,CAAC;QAC5C,MAAM,mCAAmC,CACvC,SAAS,EACT,IAAI,EACJ,aAAa,EACb,OAAO,EACP,UAAW,EACX,MAAM,CACP,CAAC;QAEF,MAAM,kBAAkB,GAAG,IAAI,CAAC,KAAK,CACnC,wBAAW,CAAC,GAAG,EAAE,GAAG,iBAAiB,CACtC,CAAC;QACF,MAAM,CAAC,IAAI,CACT,wDAAwD,IAAI,KAAK,IAAA,wBAAc,EAC7E,kBAAkB,CACnB,IAAI,CACN,CAAC;QAEF,OAAO;YACL,iBAAiB;YACjB,QAAQ,EAAE,0BAA0B,CAAC,SAAS,CAAC;YAC/C,GAAG,kCAAkC,CAAC,kBAAkB,CAAC;SAC1D,CAAC;IACJ,CAAC;IAED,MAAM,kBAAkB,GAAG,wBAAW,CAAC,GAAG,EAAE,CAAC;IAC7C,MAAM,kBAAkB,GAAG,MAAM,SAAS,CAAC,YAAY,CACrD,SAAS,EACT,SAAS,EACT,aAAa,EACb,OAAO,CACR,CAAC;IACF,MAAM,kBAAkB,GAAG,IAAI,CAAC,KAAK,CAAC,wBAAW,CAAC,GAAG,EAAE,GAAG,kBAAkB,CAAC,CAAC;IAE9E,MAAM,CAAC,IAAI,CACT,yCAAyC,kBAAkB,KAAK,IAAA,wBAAc,EAC5E,kBAAkB,CACnB,IAAI,CACN,CAAC;IAEF,IAAI,oBAA4B,CAAC;IAEjC,IAAI,CAAC;QACH,MAAM,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC;QACzC,MAAM,eAAe,GAAG,wBAAW,CAAC,GAAG,EAAE,CAAC;QAC1C,MAAM,GAAG,CAAC,OAAO,CACf,kBAAkB,EAClB,IAAI,EACJ,iBAAiB,EACjB,UAAU,EACV,MAAM,CACP,CAAC;QACF,oBAAoB,GAAG,IAAI,CAAC,KAAK,CAAC,wBAAW,CAAC,GAAG,EAAE,GAAG,eAAe,CAAC,CAAC;QACvE,MAAM,CAAC,IAAI,CACT,wCAAwC,IAAI,KAAK,IAAA,wBAAc,EAC7D,oBAAoB,CACrB,IAAI,CACN,CAAC;IACJ,CAAC;YAAS,CAAC;QACT,MAAM,IAAA,kBAAW,EAAC,kBAAkB,EAAE,uBAAuB,EAAE,MAAM,CAAC,CAAC;IACzE,CAAC;IAED,OAAO;QACL,iBAAiB;QACjB,QAAQ,EAAE,0BAA0B,CAAC,SAAS,CAAC;QAC/C,GAAG,uCAAuC,CACxC,kBAAkB,EAClB,oBAAoB,CACrB;KACF,CAAC;AACJ,CAAC;AAED,KAAK,UAAU,mCAAmC,CAChD,SAAiB,EACjB,IAAY,EACZ,aAAiC,EACjC,OAA4B,EAC5B,UAA0B,EAC1B,MAAc;IAEd,OAAO,GAAG,MAAM,CAAC,MAAM,CACrB,EAAE,YAAY,EAAE,eAAe,EAAE,EACjC,aAAa,CAAC,CAAC,CAAC,EAAE,aAAa,EAAE,CAAC,CAAC,CAAC,EAAE,EACtC,OAAO,CACR,CAAC;IACF,MAAM,QAAQ,GAAG,MAAM,IAAI,OAAO,CAAkB,CAAC,OAAO,EAAE,EAAE,CAC9D,wBAAK,CAAC,GAAG,CACP,SAAS,EACT;QACE,OAAO;QACP,aAAa,EAAE,sCAA8B;KACjB,EAC9B,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,CAClB,CACF,CAAC;IAEF,IAAI,QAAQ,CAAC,UAAU,KAAK,GAAG,EAAE,CAAC;QAChC,MAAM,IAAI,KAAK,CACb,yCAAyC,SAAS,uBAAuB,QAAQ,CAAC,UAAU,GAAG,CAChG,CAAC;IACJ,CAAC;IAED,MAAM,GAAG,CAAC,aAAa,CAAC,QAAQ,EAAE,IAAI,EAAE,UAAU,EAAE,MAAM,CAAC,CAAC;AAC9D,CAAC;AAED,8FAA8F;AAC9F,SAAgB,qBAAqB,CAAC,OAAe;IACnD,OAAO,IAAI,CAAC,IAAI,CACd,IAAA,0BAAmB,EAAC,mBAAmB,CAAC,EACxC,mBAAmB,EACnB,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,OAAO,EAChC,EAAE,CAAC,IAAI,EAAE,IAAI,EAAE,CAChB,CAAC;AACJ,CAAC;AAED,SAAgB,wBAAwB,CACtC,aAAqB,EACrB,MAAc;IAEd,MAAM,cAAc,GAAG,GAAG,aAAa,WAAW,CAAC;IACnD,EAAE,CAAC,aAAa,CAAC,cAAc,EAAE,EAAE,CAAC,CAAC;IACrC,MAAM,CAAC,KAAK,CAAC,wBAAwB,cAAc,EAAE,CAAC,CAAC;AACzD,CAAC;AAED,SAAS,0BAA0B,CAAC,GAAW;IAC7C,OAAO,CAAC,sBAAsB,EAAE,kCAAkC,CAAC,CAAC,IAAI,CACtE,CAAC,IAAI,EAAE,EAAE,CAAC,GAAG,CAAC,UAAU,CAAC,sBAAsB,IAAI,qBAAqB,CAAC,CAC1E;QACC,CAAC,CAAC,GAAG;QACL,CAAC,CAAC,iBAAiB,CAAC;AACxB,CAAC"}
\ No newline at end of file
diff --git a/src/setup-codeql.ts b/src/setup-codeql.ts
index d68ba9302..b8c915f01 100644
--- a/src/setup-codeql.ts
+++ b/src/setup-codeql.ts
@@ -23,6 +23,7 @@ import {
   downloadAndExtract,
   getToolcacheDirectory,
   ToolsDownloadStatusReport,
+  writeToolcacheMarkerFile,
 } from "./tools-download";
 import * as util from "./util";
 import { cleanUpGlob, isGoodVersion } from "./util";
@@ -571,31 +572,37 @@ export const downloadCodeQL = async function (
     };
   }
 
-  logger.debug("Caching CodeQL bundle.");
-  const toolcacheStart = performance.now();
-  const toolcachedBundlePath = await toolcache.cacheDir(
-    extractedBundlePath,
-    "CodeQL",
-    toolcacheInfo.version,
-  );
-
-  logger.info(
-    `Added CodeQL bundle to the tool cache (${formatDuration(
-      performance.now() - toolcacheStart,
-    )}).`,
-  );
+  let codeqlFolder = extractedBundlePath;
 
-  // Defensive check: we expect `cacheDir` to copy the bundle to a new location.
-  if (toolcachedBundlePath !== extractedBundlePath) {
-    await cleanUpGlob(
+  if (extractToToolcache) {
+    writeToolcacheMarkerFile(toolcacheInfo.path, logger);
+  } else {
+    logger.debug("Caching CodeQL bundle.");
+    const toolcacheStart = performance.now();
+    codeqlFolder = await toolcache.cacheDir(
       extractedBundlePath,
-      "CodeQL bundle from temporary directory",
-      logger,
+      "CodeQL",
+      toolcacheInfo.version,
+    );
+
+    logger.info(
+      `Added CodeQL bundle to the tool cache (${formatDuration(
+        performance.now() - toolcacheStart,
+      )}).`,
     );
+
+    // Defensive check: we expect `cacheDir` to copy the bundle to a new location.
+    if (codeqlFolder !== extractedBundlePath) {
+      await cleanUpGlob(
+        extractedBundlePath,
+        "CodeQL bundle from temporary directory",
+        logger,
+      );
+    }
   }
 
   return {
-    codeqlFolder: toolcachedBundlePath,
+    codeqlFolder,
     statusReport,
     toolsVersion: maybeCliVersion ?? toolcacheInfo.version,
   };
diff --git a/src/tools-download.ts b/src/tools-download.ts
index e9d43478e..9b4b96b1e 100644
--- a/src/tools-download.ts
+++ b/src/tools-download.ts
@@ -1,3 +1,4 @@
+import * as fs from "fs";
 import { IncomingMessage, OutgoingHttpHeaders, RequestOptions } from "http";
 import * as os from "os";
 import * as path from "path";
@@ -217,6 +218,15 @@ export function getToolcacheDirectory(version: string): string {
   );
 }
 
+export function writeToolcacheMarkerFile(
+  extractedPath: string,
+  logger: Logger,
+): void {
+  const markerFilePath = `${extractedPath}.complete`;
+  fs.writeFileSync(markerFilePath, "");
+  logger.debug(`Wrote marker file to ${markerFilePath}`);
+}
+
 function sanitizeUrlForStatusReport(url: string): string {
   return ["github/codeql-action", "dsp-testing/codeql-cli-nightlies"].some(
     (repo) => url.startsWith(`https://github.com/${repo}/releases/download/`),