diff --git a/lib/init-action.js b/lib/init-action.js
index 053dfe3c2..a5fcd7687 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -86442,10 +86442,15 @@ function parseQueriesFromInput(rawQueriesInput, queriesInputCombines, errorToThr
   }
   return trimmedInput.split(",").map((query) => ({ uses: query.trim() }));
 }
-function combineQueries(config, augmentationProperties) {
+function combineQueries(logger, config, augmentationProperties) {
   const result = [];
   if (augmentationProperties.repoPropertyQueries && augmentationProperties.repoPropertyQueries.input) {
     if (!augmentationProperties.repoPropertyQueries.combines) {
+      if (!isDefaultSetup()) {
+        logger.info(
+          `Queries are configured in the repository properties and don't allow combining with other query settings. Any queries configured elsewhere will be ignored.`
+        );
+      }
       return augmentationProperties.repoPropertyQueries.input;
     } else {
       result.push(...augmentationProperties.repoPropertyQueries.input);
@@ -86463,12 +86468,16 @@ function combineQueries(config, augmentationProperties) {
   }
   return result;
 }
-function generateCodeScanningConfig(originalUserInput, augmentationProperties) {
+function generateCodeScanningConfig(logger, originalUserInput, augmentationProperties) {
   const augmentedConfig = cloneObject(originalUserInput);
   augmentedConfig.queries = combineQueries(
+    logger,
     augmentedConfig,
     augmentationProperties
   );
+  logger.debug(
+    `Combined queries: ${augmentedConfig.queries?.map((q) => q.uses).join(",")}`
+  );
   if (augmentedConfig.queries?.length === 0) {
     delete augmentedConfig.queries;
   }
@@ -87614,6 +87623,7 @@ async function initActionState({
     logger
   );
   const computedConfig = generateCodeScanningConfig(
+    logger,
     userConfig,
     augmentationProperties
   );
diff --git a/src/codeql.test.ts b/src/codeql.test.ts
index b80b29725..a5422b1e3 100644
--- a/src/codeql.test.ts
+++ b/src/codeql.test.ts
@@ -496,6 +496,8 @@ const injectedConfigMacro = test.macro({
     expectedConfig: any,
   ) => {
     await util.withTmpDir(async (tempDir) => {
+      sinon.stub(actionsUtil, "isDefaultSetup").resolves(false);
+
       const runnerConstructorStub = stubToolRunnerConstructor();
       const codeqlObject = await stubCodeql();
 
@@ -505,6 +507,7 @@ const injectedConfigMacro = test.macro({
         tempDir,
       };
       thisStubConfig.computedConfig = generateCodeScanningConfig(
+        getRunnerLogger(true),
         thisStubConfig.originalUserInput,
         augmentationProperties,
       );
diff --git a/src/config-utils.ts b/src/config-utils.ts
index d20cf3bae..e6e99be3b 100644
--- a/src/config-utils.ts
+++ b/src/config-utils.ts
@@ -473,6 +473,7 @@ export async function initActionState(
   // Compute the full Code Scanning configuration that combines the configuration from the
   // configuration file / `config` input with other inputs, such as `queries`.
   const computedConfig = generateCodeScanningConfig(
+    logger,
     userConfig,
     augmentationProperties,
   );
diff --git a/src/config/db-config.ts b/src/config/db-config.ts
index c16b1f034..8e6dc501d 100644
--- a/src/config/db-config.ts
+++ b/src/config/db-config.ts
@@ -2,12 +2,14 @@ import * as path from "path";
 
 import * as semver from "semver";
 
+import { isDefaultSetup } from "../actions-util";
 import * as errorMessages from "../error-messages";
 import {
   RepositoryProperties,
   RepositoryPropertyName,
 } from "../feature-flags/properties";
 import { Language } from "../languages";
+import { Logger } from "../logging";
 import { cloneObject, ConfigurationError, prettyPrintPack } from "../util";
 
 export interface ExcludeQueryFilter {
@@ -364,11 +366,13 @@ function parseQueriesFromInput(
 /**
  * Combines queries from various configuration sources.
  *
+ * @param logger The logger to use.
  * @param config The loaded configuration file (either `config-file` or `config` input).
  * @param augmentationProperties Additional configuration data from other sources.
  * @returns Returns `augmentedConfig` with `queries` set to the computed array of queries.
  */
 function combineQueries(
+  logger: Logger,
   config: UserConfig,
   augmentationProperties: AugmentationProperties,
 ): QuerySpec[] {
@@ -383,6 +387,12 @@ function combineQueries(
     // settings. If they don't allow combining with other query configurations, return just the
     // ones configured in the repository properties.
     if (!augmentationProperties.repoPropertyQueries.combines) {
+      if (!isDefaultSetup()) {
+        logger.info(
+          `Queries are configured in the repository properties and don't allow combining with other query settings. ` +
+            `Any queries configured elsewhere will be ignored.`,
+        );
+      }
       return augmentationProperties.repoPropertyQueries.input;
     } else {
       // Otherwise, add them to the query array and continue.
@@ -414,6 +424,7 @@ function combineQueries(
 }
 
 export function generateCodeScanningConfig(
+  logger: Logger,
   originalUserInput: UserConfig,
   augmentationProperties: AugmentationProperties,
 ): UserConfig {
@@ -422,9 +433,13 @@ export function generateCodeScanningConfig(
 
   // Inject the queries from the input
   augmentedConfig.queries = combineQueries(
+    logger,
     augmentedConfig,
     augmentationProperties,
   );
+  logger.debug(
+    `Combined queries: ${augmentedConfig.queries?.map((q) => q.uses).join(",")}`,
+  );
   if (augmentedConfig.queries?.length === 0) {
     delete augmentedConfig.queries;
   }