diff --git a/lib/analyze-action-post.js b/lib/analyze-action-post.js
index d815da082f..de3b89b111 100644
--- a/lib/analyze-action-post.js
+++ b/lib/analyze-action-post.js
@@ -120102,6 +120102,8 @@ var featureConfig = {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/analyze-action.js b/lib/analyze-action.js
index 5dcfd5062e..d80524b30c 100644
--- a/lib/analyze-action.js
+++ b/lib/analyze-action.js
@@ -89370,6 +89370,8 @@ async function cachePrefix(codeql, language) {
 }
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/autobuild-action.js b/lib/autobuild-action.js
index 2655e43157..e9807b9d69 100644
--- a/lib/autobuild-action.js
+++ b/lib/autobuild-action.js
@@ -84416,6 +84416,8 @@ var GitHubFeatureFlags = class {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/init-action-post.js b/lib/init-action-post.js
index c238f7d069..45f90f0358 100644
--- a/lib/init-action-post.js
+++ b/lib/init-action-post.js
@@ -123766,6 +123766,8 @@ ${jsonContents}`
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/init-action.js b/lib/init-action.js
index 6de0e4e2db..ff9b723332 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -86653,6 +86653,8 @@ async function cachePrefix(codeql, language) {
 }
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 async function getSupportedLanguageMap(codeql, logger) {
   const resolveSupportedLanguagesUsingCli = await codeql.supportsFeature(
     "builtinExtractorsSpecifyDefaultQueries" /* BuiltinExtractorsSpecifyDefaultQueries */
@@ -86924,18 +86926,28 @@ async function getOverlayDatabaseMode(codeql, features, languages, sourceRoot, b
     languages,
     codeScanningConfig
   )) {
-    if (isAnalyzingPullRequest()) {
-      overlayDatabaseMode = "overlay" /* Overlay */;
-      useOverlayDatabaseCaching = true;
+    const diskUsage = await checkDiskUsage(logger);
+    if (diskUsage === void 0 || diskUsage.numAvailableBytes < OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES) {
+      const diskSpaceMb = diskUsage === void 0 ? 0 : Math.round(diskUsage.numAvailableBytes / 1e6);
+      overlayDatabaseMode = "none" /* None */;
+      useOverlayDatabaseCaching = false;
       logger.info(
-        `Setting overlay database mode to ${overlayDatabaseMode} with caching because we are analyzing a pull request.`
-      );
-    } else if (await isAnalyzingDefaultBranch()) {
-      overlayDatabaseMode = "overlay-base" /* OverlayBase */;
-      useOverlayDatabaseCaching = true;
-      logger.info(
-        `Setting overlay database mode to ${overlayDatabaseMode} with caching because we are analyzing the default branch.`
+        `Setting overlay database mode to ${overlayDatabaseMode} due to insufficient disk space (${diskSpaceMb} MB).`
       );
+    } else {
+      if (isAnalyzingPullRequest()) {
+        overlayDatabaseMode = "overlay" /* Overlay */;
+        useOverlayDatabaseCaching = true;
+        logger.info(
+          `Setting overlay database mode to ${overlayDatabaseMode} with caching because we are analyzing a pull request.`
+        );
+      } else if (await isAnalyzingDefaultBranch()) {
+        overlayDatabaseMode = "overlay-base" /* OverlayBase */;
+        useOverlayDatabaseCaching = true;
+        logger.info(
+          `Setting overlay database mode to ${overlayDatabaseMode} with caching because we are analyzing the default branch.`
+        );
+      }
     }
   }
   const nonOverlayAnalysis = {
diff --git a/lib/resolve-environment-action.js b/lib/resolve-environment-action.js
index 8a757d8c61..8bfc24ca03 100644
--- a/lib/resolve-environment-action.js
+++ b/lib/resolve-environment-action.js
@@ -84142,6 +84142,8 @@ var featureConfig = {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/setup-codeql-action.js b/lib/setup-codeql-action.js
index 31f135f53c..ccd2157ad7 100644
--- a/lib/setup-codeql-action.js
+++ b/lib/setup-codeql-action.js
@@ -84587,6 +84587,8 @@ var PACK_IDENTIFIER_PATTERN = (function() {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/start-proxy-action-post.js b/lib/start-proxy-action-post.js
index 86991078ab..c22306a3b4 100644
--- a/lib/start-proxy-action-post.js
+++ b/lib/start-proxy-action-post.js
@@ -119508,6 +119508,8 @@ var featureConfig = {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/start-proxy-action.js b/lib/start-proxy-action.js
index 3b6d4deca5..e54c456eb5 100644
--- a/lib/start-proxy-action.js
+++ b/lib/start-proxy-action.js
@@ -100170,6 +100170,8 @@ var featureConfig = {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/upload-lib.js b/lib/upload-lib.js
index e9e0a6747c..3b951984b5 100644
--- a/lib/upload-lib.js
+++ b/lib/upload-lib.js
@@ -87226,6 +87226,8 @@ ${jsonContents}`
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/upload-sarif-action-post.js b/lib/upload-sarif-action-post.js
index 96a6bc64be..4c6f138026 100644
--- a/lib/upload-sarif-action-post.js
+++ b/lib/upload-sarif-action-post.js
@@ -119674,6 +119674,8 @@ var featureConfig = {
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/lib/upload-sarif-action.js b/lib/upload-sarif-action.js
index 6db9c67bdf..b6eaf19a0f 100644
--- a/lib/upload-sarif-action.js
+++ b/lib/upload-sarif-action.js
@@ -87307,6 +87307,8 @@ ${jsonContents}`
 var actionsCache2 = __toESM(require_cache3());
 
 // src/config-utils.ts
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 2e4;
+var OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES = OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1e6;
 var OVERLAY_ANALYSIS_FEATURES = {
   actions: "overlay_analysis_actions" /* OverlayAnalysisActions */,
   cpp: "overlay_analysis_cpp" /* OverlayAnalysisCpp */,
diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index da58dd8b1b..b9407152b9 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -37,7 +37,9 @@ import {
   ConfigurationError,
   withTmpDir,
   BuildMode,
+  DiskUsage,
 } from "./util";
+import * as util from "./util";
 
 setupTests(test);
 
@@ -995,6 +997,7 @@ interface OverlayDatabaseModeTestSetup {
   codeqlVersion: string;
   gitRoot: string | undefined;
   codeScanningConfig: configUtils.UserConfig;
+  diskUsage: DiskUsage | undefined;
 }
 
 const defaultOverlayDatabaseModeTestSetup: OverlayDatabaseModeTestSetup = {
@@ -1007,6 +1010,10 @@ const defaultOverlayDatabaseModeTestSetup: OverlayDatabaseModeTestSetup = {
   codeqlVersion: CODEQL_OVERLAY_MINIMUM_VERSION,
   gitRoot: "/some/git/root",
   codeScanningConfig: {},
+  diskUsage: {
+    numAvailableBytes: 50_000_000_000,
+    numTotalBytes: 100_000_000_000,
+  },
 };
 
 const getOverlayDatabaseModeMacro = test.macro({
@@ -1039,6 +1046,8 @@ const getOverlayDatabaseModeMacro = test.macro({
             setup.overlayDatabaseEnvVar;
         }
 
+        sinon.stub(util, "checkDiskUsage").resolves(setup.diskUsage);
+
         // Mock feature flags
         const features = createFeatures(setup.features);
 
@@ -1196,6 +1205,45 @@ test(
   },
 );
 
+test(
+  getOverlayDatabaseModeMacro,
+  "No overlay-base database on default branch if runner disk space is too low",
+  {
+    languages: [KnownLanguage.javascript],
+    features: [
+      Feature.OverlayAnalysis,
+      Feature.OverlayAnalysisCodeScanningJavascript,
+    ],
+    isDefaultBranch: true,
+    diskUsage: {
+      numAvailableBytes: 1_000_000_000,
+      numTotalBytes: 100_000_000_000,
+    },
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.None,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
+test(
+  getOverlayDatabaseModeMacro,
+  "No overlay-base database on default branch if we can't determine runner disk space",
+  {
+    languages: [KnownLanguage.javascript],
+    features: [
+      Feature.OverlayAnalysis,
+      Feature.OverlayAnalysisCodeScanningJavascript,
+    ],
+    isDefaultBranch: true,
+    diskUsage: undefined,
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.None,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
 test(
   getOverlayDatabaseModeMacro,
   "No overlay-base database on default branch when code-scanning feature enabled with disable-default-queries",
@@ -1366,6 +1414,45 @@ test(
   },
 );
 
+test(
+  getOverlayDatabaseModeMacro,
+  "No overlay analysis on PR if runner disk space is too low",
+  {
+    languages: [KnownLanguage.javascript],
+    features: [
+      Feature.OverlayAnalysis,
+      Feature.OverlayAnalysisCodeScanningJavascript,
+    ],
+    isPullRequest: true,
+    diskUsage: {
+      numAvailableBytes: 1_000_000_000,
+      numTotalBytes: 100_000_000_000,
+    },
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.None,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
+test(
+  getOverlayDatabaseModeMacro,
+  "No overlay analysis on PR if we can't determine runner disk space",
+  {
+    languages: [KnownLanguage.javascript],
+    features: [
+      Feature.OverlayAnalysis,
+      Feature.OverlayAnalysisCodeScanningJavascript,
+    ],
+    isPullRequest: true,
+    diskUsage: undefined,
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.None,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
 test(
   getOverlayDatabaseModeMacro,
   "No overlay analysis on PR when code-scanning feature enabled with disable-default-queries",
@@ -1500,6 +1587,19 @@ test(
   },
 );
 
+test(
+  getOverlayDatabaseModeMacro,
+  "Overlay PR analysis by env on a runner with low disk space",
+  {
+    overlayDatabaseEnvVar: "overlay",
+    diskUsage: { numAvailableBytes: 0, numTotalBytes: 100_000_000_000 },
+  },
+  {
+    overlayDatabaseMode: OverlayDatabaseMode.Overlay,
+    useOverlayDatabaseCaching: false,
+  },
+);
+
 test(
   getOverlayDatabaseModeMacro,
   "Overlay PR analysis by feature flag",
diff --git a/src/config-utils.ts b/src/config-utils.ts
index fa88d4b4a5..2572573448 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -43,10 +43,22 @@ import {
   codeQlVersionAtLeast,
   cloneObject,
   isDefined,
+  checkDiskUsage,
 } from "./util";
 
 export * from "./config/db-config";
 
+/**
+ * The minimum available disk space (in MB) required to perform overlay analysis.
+ * If the available disk space on the runner is below the threshold when deciding
+ * whether to perform overlay analysis, then the action will not perform overlay
+ * analysis unless overlay analysis has been explicitly enabled via environment
+ * variable.
+ */
+const OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB = 20000;
+const OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES =
+  OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_MB * 1_000_000;
+
 export type RegistryConfigWithCredentials = RegistryConfigNoCredentials & {
   // Token to use when downloading packs from this registry.
   token: string;
@@ -675,20 +687,37 @@ export async function getOverlayDatabaseMode(
       codeScanningConfig,
     )
   ) {
-    if (isAnalyzingPullRequest()) {
-      overlayDatabaseMode = OverlayDatabaseMode.Overlay;
-      useOverlayDatabaseCaching = true;
-      logger.info(
-        `Setting overlay database mode to ${overlayDatabaseMode} ` +
-          "with caching because we are analyzing a pull request.",
-      );
-    } else if (await isAnalyzingDefaultBranch()) {
-      overlayDatabaseMode = OverlayDatabaseMode.OverlayBase;
-      useOverlayDatabaseCaching = true;
+    const diskUsage = await checkDiskUsage(logger);
+    if (
+      diskUsage === undefined ||
+      diskUsage.numAvailableBytes < OVERLAY_MINIMUM_AVAILABLE_DISK_SPACE_BYTES
+    ) {
+      const diskSpaceMb =
+        diskUsage === undefined
+          ? 0
+          : Math.round(diskUsage.numAvailableBytes / 1_000_000);
+      overlayDatabaseMode = OverlayDatabaseMode.None;
+      useOverlayDatabaseCaching = false;
       logger.info(
         `Setting overlay database mode to ${overlayDatabaseMode} ` +
-          "with caching because we are analyzing the default branch.",
+          `due to insufficient disk space (${diskSpaceMb} MB).`,
       );
+    } else {
+      if (isAnalyzingPullRequest()) {
+        overlayDatabaseMode = OverlayDatabaseMode.Overlay;
+        useOverlayDatabaseCaching = true;
+        logger.info(
+          `Setting overlay database mode to ${overlayDatabaseMode} ` +
+            "with caching because we are analyzing a pull request.",
+        );
+      } else if (await isAnalyzingDefaultBranch()) {
+        overlayDatabaseMode = OverlayDatabaseMode.OverlayBase;
+        useOverlayDatabaseCaching = true;
+        logger.info(
+          `Setting overlay database mode to ${overlayDatabaseMode} ` +
+            "with caching because we are analyzing the default branch.",
+        );
+      }
     }
   }