diff --git a/lib/init-action.js b/lib/init-action.js
index dbd5a8926..dab7782f8 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -90701,6 +90701,7 @@ exec ${goBinaryPath} "$@"`
   } finally {
     logUnwrittenDiagnostics();
   }
+  await saveConfig(config, logger);
   await sendCompletedStatusReport(
     startedAt,
     config,
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 7bdc29a2e..c84e9ecfc 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -1289,7 +1289,7 @@ export function getPathToParsedConfigFile(tempDir: string): string {
 /**
  * Store the given config to the path returned from getPathToParsedConfigFile.
  */
-async function saveConfig(config: Config, logger: Logger) {
+export async function saveConfig(config: Config, logger: Logger) {
   const configString = JSON.stringify(config);
   const configFile = getPathToParsedConfigFile(config.tempDir);
   fs.mkdirSync(path.dirname(configFile), { recursive: true });
diff --git a/src/init-action.ts b/src/init-action.ts
index 8c9e2f36b..4e9446b84 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -680,6 +680,12 @@ async function run() {
   } finally {
     logUnwrittenDiagnostics();
   }
+
+  // We may have updated the config returned from `initConfig`, e.g. to revert
+  // to `OverlayDatabaseMode.None` if we failed to download an overlay-base
+  // database. So we save the config again, to ensure that the `analyze` step
+  // reads the correct config.
+  await configUtils.saveConfig(config, logger);
   await sendCompletedStatusReport(
     startedAt,
     config,