diff --git a/init/action.yml b/init/action.yml
index bb343a90b..49a3cc650 100644
--- a/init/action.yml
+++ b/init/action.yml
@@ -97,7 +97,7 @@ inputs:
     description: Comma-separated list of additional queries to run. By default, this overrides the same setting in a configuration file; prefix with "+" to use both sets of queries.
     required: false
   quality-queries:
-    description: '[Internal] Comma-separated list of code quality queries to run.'
+    description: '[Internal] DEPRECATED. Comma-separated list of code quality queries to run.'
     required: false
   packs:
     description: >-
diff --git a/lib/init-action.js b/lib/init-action.js
index 1f792b82a..452a305ab 100644
--- a/lib/init-action.js
+++ b/lib/init-action.js
@@ -90342,11 +90342,17 @@ async function run() {
         logger.info("Experimental Rust analysis enabled");
       }
     }
+    const qualityQueriesInput = getOptionalInput("quality-queries");
+    if (qualityQueriesInput !== void 0) {
+      logger.warning(
+        "The `quality-queries` input is deprecated and will be removed in a future version of the CodeQL Action. Use the `analysis-kinds` input to configure different analysis kinds instead."
+      );
+    }
     config = await initConfig2({
       analysisKindsInput: getRequiredInput("analysis-kinds"),
       languagesInput: getOptionalInput("languages"),
       queriesInput: getOptionalInput("queries"),
-      qualityQueriesInput: getOptionalInput("quality-queries"),
+      qualityQueriesInput,
       packsInput: getOptionalInput("packs"),
       buildModeInput: getOptionalInput("build-mode"),
       configFile,
diff --git a/src/init-action.ts b/src/init-action.ts
index 04c6bafe1..df22fe6a5 100644
--- a/src/init-action.ts
+++ b/src/init-action.ts
@@ -384,11 +384,21 @@ async function run() {
       }
     }
 
+    // Warn that `quality-queries` is deprecated if there is an argument for it.
+    const qualityQueriesInput = getOptionalInput("quality-queries");
+
+    if (qualityQueriesInput !== undefined) {
+      logger.warning(
+        "The `quality-queries` input is deprecated and will be removed in a future version of the CodeQL Action. " +
+          "Use the `analysis-kinds` input to configure different analysis kinds instead.",
+      );
+    }
+
     config = await initConfig({
       analysisKindsInput: getRequiredInput("analysis-kinds"),
       languagesInput: getOptionalInput("languages"),
       queriesInput: getOptionalInput("queries"),
-      qualityQueriesInput: getOptionalInput("quality-queries"),
+      qualityQueriesInput,
       packsInput: getOptionalInput("packs"),
       buildModeInput: getOptionalInput("build-mode"),
       configFile,