diff --git a/src/codeql.test.ts b/src/codeql.test.ts
index 24d5fe49b..053c99a16 100644
--- a/src/codeql.test.ts
+++ b/src/codeql.test.ts
@@ -24,7 +24,6 @@ import { DocUrl } from "./doc-url";
 import { FeatureEnablement } from "./feature-flags";
 import { Language } from "./languages";
 import { getRunnerLogger } from "./logging";
-import { OverlayDatabaseMode } from "./overlay-database-utils";
 import { ToolsSource } from "./setup-codeql";
 import {
   setupTests,
@@ -515,7 +514,6 @@ const injectedConfigMacro = test.macro({
         "",
         undefined,
         undefined,
-        OverlayDatabaseMode.None,
         getRunnerLogger(true),
       );
 
@@ -726,7 +724,6 @@ test("passes a code scanning config AND qlconfig to the CLI", async (t: Executio
       "",
       undefined,
       "/path/to/qlconfig.yml",
-      OverlayDatabaseMode.None,
       getRunnerLogger(true),
     );
 
@@ -756,7 +753,6 @@ test("does not pass a qlconfig to the CLI when it is undefined", async (t: Execu
       "",
       undefined,
       undefined, // undefined qlconfigFile
-      OverlayDatabaseMode.None,
       getRunnerLogger(true),
     );
 
@@ -1010,7 +1006,6 @@ test("Avoids duplicating --overwrite flag if specified in CODEQL_ACTION_EXTRA_OP
     "sourceRoot",
     undefined,
     undefined,
-    OverlayDatabaseMode.None,
     getRunnerLogger(false),
   );
 
diff --git a/src/codeql.ts b/src/codeql.ts
index 07b763b59..0cc917c22 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -87,7 +87,6 @@ export interface CodeQL {
     sourceRoot: string,
     processName: string | undefined,
     qlconfigFile: string | undefined,
-    overlayDatabaseMode: OverlayDatabaseMode,
     logger: Logger,
   ): Promise<void>;
   /**
@@ -564,7 +563,6 @@ export async function getCodeQLForCmd(
       sourceRoot: string,
       processName: string | undefined,
       qlconfigFile: string | undefined,
-      overlayDatabaseMode: OverlayDatabaseMode,
       logger: Logger,
     ) {
       const extraArgs = config.languages.map(
@@ -602,6 +600,8 @@ export async function getCodeQLForCmd(
         ? "--force-overwrite"
         : "--overwrite";
 
+      const overlayDatabaseMode =
+        config.augmentationProperties.overlayDatabaseMode;
       if (overlayDatabaseMode === OverlayDatabaseMode.Overlay) {
         const overlayChangesFile = await writeOverlayChangesFile(
           config,
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 9aea68904..7d05ec357 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -695,6 +695,7 @@ export async function calculateAugmentation(
     buildMode,
     logger,
   );
+  logger.info(`Using overlay database mode: ${overlayDatabaseMode}`);
 
   const qualityQueriesInput = parseQueriesFromInput(
     rawQualityQueriesInput,
diff --git a/src/init-action.ts b/src/init-action.ts
index 74327d4f6..a3837cbd2 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -36,7 +36,6 @@ import { Feature, featureConfig, Features } from "./feature-flags";
 import {
   checkInstallPython311,
   cleanupDatabaseClusterDirectory,
-  getOverlayDatabaseMode,
   initCodeQL,
   initConfig,
   runInit,
@@ -399,15 +398,10 @@ async function run() {
   }
 
   try {
-    const overlayDatabaseMode = await getOverlayDatabaseMode(
-      (await codeql.getVersion()).version,
-      config,
-      sourceRoot,
-      logger,
-    );
-    logger.info(`Using overlay database mode: ${overlayDatabaseMode}`);
-
-    if (overlayDatabaseMode !== OverlayDatabaseMode.Overlay) {
+    if (
+      config.augmentationProperties.overlayDatabaseMode !==
+      OverlayDatabaseMode.Overlay
+    ) {
       cleanupDatabaseClusterDirectory(config, logger);
     }
 
@@ -679,7 +673,6 @@ async function run() {
       "Runner.Worker.exe",
       getOptionalInput("registries"),
       apiDetails,
-      overlayDatabaseMode,
       logger,
     );
     if (tracerConfig !== undefined) {
diff --git a/src/init.ts b/src/init.ts
index bad26bb78..b49aac25f 100644
--- a/src/init.ts
+++ b/src/init.ts
@@ -3,20 +3,14 @@ import * as path from "path";
 
 import * as toolrunner from "@actions/exec/lib/toolrunner";
 import * as io from "@actions/io";
-import * as semver from "semver";
 
 import { getOptionalInput, isSelfHostedRunner } from "./actions-util";
 import { GitHubApiCombinedDetails, GitHubApiDetails } from "./api-client";
 import { CodeQL, setupCodeQL } from "./codeql";
 import * as configUtils from "./config-utils";
 import { CodeQLDefaultVersionInfo, FeatureEnablement } from "./feature-flags";
-import { getGitRoot } from "./git-utils";
 import { Language } from "./languages";
 import { Logger, withGroupAsync } from "./logging";
-import {
-  CODEQL_OVERLAY_MINIMUM_VERSION,
-  OverlayDatabaseMode,
-} from "./overlay-database-utils";
 import { ToolsSource } from "./setup-codeql";
 import { ZstdAvailability } from "./tar";
 import { ToolsDownloadStatusReport } from "./tools-download";
@@ -74,47 +68,6 @@ export async function initConfig(
   });
 }
 
-export async function getOverlayDatabaseMode(
-  codeqlVersion: string,
-  config: configUtils.Config,
-  sourceRoot: string,
-  logger: Logger,
-): Promise<OverlayDatabaseMode> {
-  const overlayDatabaseMode = process.env.CODEQL_OVERLAY_DATABASE_MODE;
-
-  if (
-    overlayDatabaseMode === OverlayDatabaseMode.Overlay ||
-    overlayDatabaseMode === OverlayDatabaseMode.OverlayBase
-  ) {
-    if (config.buildMode !== util.BuildMode.None) {
-      logger.warning(
-        `Cannot build an ${overlayDatabaseMode} database because ` +
-          `build-mode is set to "${config.buildMode}" instead of "none". ` +
-          "Falling back to creating a normal full database instead.",
-      );
-      return OverlayDatabaseMode.None;
-    }
-    if (semver.lt(codeqlVersion, CODEQL_OVERLAY_MINIMUM_VERSION)) {
-      logger.warning(
-        `Cannot build an ${overlayDatabaseMode} database because ` +
-          `the CodeQL CLI is older than ${CODEQL_OVERLAY_MINIMUM_VERSION}. ` +
-          "Falling back to creating a normal full database instead.",
-      );
-      return OverlayDatabaseMode.None;
-    }
-    if ((await getGitRoot(sourceRoot)) === undefined) {
-      logger.warning(
-        `Cannot build an ${overlayDatabaseMode} database because ` +
-          `the source root "${sourceRoot}" is not inside a git repository. ` +
-          "Falling back to creating a normal full database instead.",
-      );
-      return OverlayDatabaseMode.None;
-    }
-    return overlayDatabaseMode as OverlayDatabaseMode;
-  }
-  return OverlayDatabaseMode.None;
-}
-
 export async function runInit(
   codeql: CodeQL,
   config: configUtils.Config,
@@ -122,7 +75,6 @@ export async function runInit(
   processName: string | undefined,
   registriesInput: string | undefined,
   apiDetails: GitHubApiCombinedDetails,
-  overlayDatabaseMode: OverlayDatabaseMode,
   logger: Logger,
 ): Promise<TracerConfig | undefined> {
   fs.mkdirSync(config.dbLocation, { recursive: true });
@@ -146,7 +98,6 @@ export async function runInit(
         sourceRoot,
         processName,
         qlconfigFile,
-        overlayDatabaseMode,
         logger,
       ),
   );