diff --git a/src/config-utils.test.ts b/src/config-utils.test.ts
index 8ef35e4d4..75461b90e 100644
--- a/src/config-utils.test.ts
+++ b/src/config-utils.test.ts
@@ -589,16 +589,15 @@ test("Using config input and file together, config input should be used.", async
     // Only JS, python packs will be ignored
     const languagesInput = "javascript";
 
-    const config = await configUtils.initConfig(
-      createTestInitConfigInputs({
-        languagesInput,
-        configFile: configFilePath,
-        configInput,
-        tempDir,
-        workspacePath: tempDir,
-      }),
-      codeql,
-    );
+    const inputs = createTestInitConfigInputs({
+      languagesInput,
+      configFile: configFilePath,
+      configInput,
+      tempDir,
+      workspacePath: tempDir,
+    });
+    configUtils.amendInputConfigFile(inputs, inputs.logger);
+    const config = await configUtils.initConfig(inputs, codeql);
 
     t.deepEqual(config.originalUserInput, yaml.load(configInput));
   });
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 55867138c..984476f97 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -569,6 +569,30 @@ async function downloadCacheWithTime(
   return { trapCaches, trapCacheDownloadTime };
 }
 
+/**
+ * Amends the input config file if configInput is provided.
+ * If configInput is set, it takes precedence over configFile.
+ *
+ * This function should be called only once on any specific `InitConfigInputs`
+ * object. Otherwise it could emit a false warning.
+ */
+export function amendInputConfigFile(
+  inputs: InitConfigInputs,
+  logger: Logger,
+): void {
+  // if configInput is set, it takes precedence over configFile
+  if (inputs.configInput) {
+    if (inputs.configFile) {
+      logger.warning(
+        `Both a config file and config input were provided. Ignoring config file.`,
+      );
+    }
+    inputs.configFile = userConfigFromActionPath(inputs.tempDir);
+    fs.writeFileSync(inputs.configFile, inputs.configInput);
+    logger.debug(`Using config from action input: ${inputs.configFile}`);
+  }
+}
+
 async function loadUserConfig(
   configFile: string,
   workspacePath: string,
@@ -839,18 +863,6 @@ export async function initConfig(
 ): Promise<Config> {
   const { logger, tempDir } = inputs;
 
-  // if configInput is set, it takes precedence over configFile
-  if (inputs.configInput) {
-    if (inputs.configFile) {
-      logger.warning(
-        `Both a config file and config input were provided. Ignoring config file.`,
-      );
-    }
-    inputs.configFile = userConfigFromActionPath(tempDir);
-    fs.writeFileSync(inputs.configFile, inputs.configInput);
-    logger.debug(`Using config from action input: ${inputs.configFile}`);
-  }
-
   let userConfig: UserConfig = {};
   if (!inputs.configFile) {
     logger.debug("No configuration file was provided");
diff --git a/src/init-action.ts b/src/init-action.ts
index b897a22cf..9b1f6713c 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -265,6 +265,7 @@ async function run() {
       repositoryProperties,
       logger,
     };
+    configUtils.amendInputConfigFile(inputs, logger);
 
     const codeQLDefaultVersionInfo = await features.getDefaultCliVersion(
       gitHubVersion.type,