diff --git a/lib/entry-points.js b/lib/entry-points.js
index 5fde8a09a..de7255217 100644
--- a/lib/entry-points.js
+++ b/lib/entry-points.js
@@ -174622,7 +174622,9 @@ async function initActionState({
     useOverlayDatabaseCaching: false,
     overlayModeSetExplicitly: false,
     repositoryProperties,
-    enableFileCoverageInformation
+    enableFileCoverageInformation,
+    // We don't set this to `true` until `init` is successful.
+    successfullyInitialised: false
   };
 }
 async function downloadCacheWithTime(codeQL, languages, logger2, repositoryRoot) {
@@ -177448,12 +177450,14 @@ async function getCodeQLForCmd(logger2, cmd, checkVersion) {
     async diagnosticsExport(sarifFile, automationDetailsId, config, diagnosticDir) {
       let configPath = getGeneratedCodeScanningConfigPath(config);
       if (!fs17.existsSync(configPath)) {
-        logger2.warning(
-          [
-            `Expected a configuration file at '${configPath}', which does not exist.`,
-            "Continuing with diagnostics export anyway, without a configuration file."
-          ].join(" ")
-        );
+        if (config.successfullyInitialised) {
+          logger2.warning(
+            [
+              `Expected a configuration file at '${configPath}', which does not exist.`,
+              "Continuing with diagnostics export anyway, without a configuration file."
+            ].join(" ")
+          );
+        }
         configPath = void 0;
       }
       const args = [
@@ -186923,6 +186927,7 @@ exec ${goBinaryPath} "$@"`
       );
     }
     flushDiagnostics(actionState, config);
+    config.successfullyInitialised = true;
     await saveConfig(config, logger2);
     core19.setOutput("codeql-path", config.codeQLCmd);
     core19.setOutput("codeql-version", (await codeql.getVersion()).version);
diff --git a/src/codeql.ts b/src/codeql.ts
index b88144a25..9824b7e4f 100644
--- a/src/codeql.ts
+++ b/src/codeql.ts
@@ -928,12 +928,17 @@ async function getCodeQLForCmd(
         getGeneratedCodeScanningConfigPath(config);
 
       if (!fs.existsSync(configPath)) {
-        logger.warning(
-          [
-            `Expected a configuration file at '${configPath}', which does not exist.`,
-            "Continuing with diagnostics export anyway, without a configuration file.",
-          ].join(" "),
-        );
+        // Warn if there is no configuration file, even though `config` claims that `init`
+        // was successful. This shouldn't be happening.
+        if (config.successfullyInitialised) {
+          logger.warning(
+            [
+              `Expected a configuration file at '${configPath}', which does not exist.`,
+              "Continuing with diagnostics export anyway, without a configuration file.",
+            ].join(" "),
+          );
+        }
+
         configPath = undefined;
       }
 
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 7bb7a37c0..12c1024f8 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -465,6 +465,8 @@ export async function initActionState(
     overlayModeSetExplicitly: false,
     repositoryProperties,
     enableFileCoverageInformation,
+    // We don't set this to `true` until `init` is successful.
+    successfullyInitialised: false,
   };
 }
 
diff --git a/src/config/action-config.ts b/src/config/action-config.ts
index 4990ba675..9daf966ee 100644
--- a/src/config/action-config.ts
+++ b/src/config/action-config.ts
@@ -130,6 +130,9 @@ export interface Config {
    * Whether to enable file coverage information.
    */
   enableFileCoverageInformation: boolean;
+
+  /** Whether the analysis was successfully initialised using the configuration. */
+  successfullyInitialised: boolean;
 }
 
 /** Properties available in `Config`. */
diff --git a/src/init-action.ts b/src/init-action.ts
index bd5ed3395..ceffe9d6e 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -775,6 +775,7 @@ async function run(
     // may have updated the config returned from `initConfig`, e.g. to revert to
     // `OverlayDatabaseMode.None` if we failed to download an overlay-base
     // database.
+    config.successfullyInitialised = true;
     await configUtils.saveConfig(config, logger);
 
     core.setOutput("codeql-path", config.codeQLCmd);
diff --git a/src/testing-utils.ts b/src/testing-utils.ts
index 8c38187c4..adcdfe3e4 100644
--- a/src/testing-utils.ts
+++ b/src/testing-utils.ts
@@ -1031,6 +1031,7 @@ export function createTestConfig(overrides: Partial<Config>): Config {
       overlayModeSetExplicitly: false,
       repositoryProperties: {},
       enableFileCoverageInformation: true,
+      successfullyInitialised: false,
     } satisfies Config,
     overrides,
   );