diff --git a/lib/init-action.js b/lib/init-action.js
index 381d2061e..e76379f64 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -87612,8 +87612,8 @@ async function initConfig(inputs) {
   const config = await initActionState(inputs, userConfig);
   if (config.analysisKinds.length === 1 && isCodeQualityEnabled(config)) {
     if (hasQueryCustomisation(config.computedConfig)) {
-      logger.warning(
-        "Query customizations will be ignored, because only `code-quality` analysis is enabled."
+      throw new ConfigurationError(
+        "Query customizations are unsupported, because only `code-quality` analysis is enabled."
       );
     }
     const queries = codeQualityQueries.map((v) => ({ uses: v }));
diff --git a/src/config-utils.ts b/src/config-utils.ts
index 626cd4b49..16144398f 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -1137,8 +1137,8 @@ export async function initConfig(inputs: InitConfigInputs): Promise<Config> {
   if (config.analysisKinds.length === 1 && isCodeQualityEnabled(config)) {
     // Warn if any query customisations are present in the computed configuration.
     if (hasQueryCustomisation(config.computedConfig)) {
-      logger.warning(
-        "Query customizations will be ignored, because only `code-quality` analysis is enabled.",
+      throw new ConfigurationError(
+        "Query customizations are unsupported, because only `code-quality` analysis is enabled.",
       );
     }