diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8ff44ec9b7..08d6d04ffd 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,7 +4,7 @@ See the [releases page](https://github.com/github/codeql-action/releases) for th
 
 ## [UNRELEASED]
 
-No user facing changes.
+- The `cleanup-level` input to the `analyze` Action is now deprecated. The CodeQL Action has not written intermediate results to the database since version 2.2.5, so this option now has little to no practical use. [#2998](https://github.com/github/codeql-action/pull/2998)
 
 ## 3.29.5 - 29 Jul 2025
 
diff --git a/analyze/action.yml b/analyze/action.yml
index 7fec8fb44f..232227dcc6 100644
--- a/analyze/action.yml
+++ b/analyze/action.yml
@@ -19,9 +19,10 @@ inputs:
     # If changing this, make sure to update workflow.ts accordingly.
     default: "always"
   cleanup-level:
-    description: "Level of cleanup to perform on CodeQL databases at the end of the analyze step. This should either be 'none' to skip cleanup, or be a valid argument for the --cache-cleanup flag of the CodeQL CLI command 'codeql database cleanup' as documented at https://codeql.github.com/docs/codeql-cli/manual/database-cleanup"
+    description: >-
+      DEPRECATED. This option is ignored since, for performance reasons, the CodeQL Action no longer saves
+      intermediate results during evaluation.
     required: false
-    default: "brutal"
   ram:
     description: >-
       The amount of memory in MB that can be used by CodeQL for database finalization and query execution.
diff --git a/lib/analyze-action-env.test.js b/lib/analyze-action-env.test.js
index 22f14ff5ea..576edecef0 100644
--- a/lib/analyze-action-env.test.js
+++ b/lib/analyze-action-env.test.js
@@ -78,7 +78,6 @@ const util = __importStar(require("./util"));
         requiredInputStub.withArgs("upload-database").returns("false");
         requiredInputStub.withArgs("output").returns("out");
         const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
-        optionalInputStub.withArgs("cleanup-level").returns("none");
         optionalInputStub.withArgs("expect-error").returns("false");
         sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
         (0, testing_utils_1.setupActionsVars)(tmpDir, tmpDir);
diff --git a/lib/analyze-action-env.test.js.map b/lib/analyze-action-env.test.js.map
index 82e6f5995d..4760c957b9 100644
--- a/lib/analyze-action-env.test.js.map
+++ b/lib/analyze-action-env.test.js.map
@@ -1 +1 @@
-{"version":3,"file":"analyze-action-env.test.js","sourceRoot":"","sources":["../src/analyze-action-env.test.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,6CAA+B;AAE/B,4DAA8C;AAC9C,mDAAqC;AACrC,kDAAoC;AACpC,4DAA8C;AAC9C,sDAAwC;AACxC,8DAAgD;AAChD,mDAIyB;AACzB,6CAA+B;AAE/B,IAAA,0BAAU,EAAC,aAAI,CAAC,CAAC;AAEjB,4EAA4E;AAC5E,4EAA4E;AAC5E,+EAA+E;AAC/E,+EAA+E;AAC/E,gFAAgF;AAChF,iCAAiC;AAEjC,IAAA,aAAI,EAAC,8DAA8D,EAAE,KAAK,EAAE,CAAC,EAAE,EAAE;IAC/E,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QACrC,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,GAAG,IAAI,CAAC,iBAAiB,CAAC;QAC1D,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,GAAG,sCAAsC,CAAC;QAC1E,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,GAAG,wBAAwB,CAAC;QACzD,KAAK;aACF,IAAI,CAAC,YAAY,EAAE,wBAAwB,CAAC;aAC5C,QAAQ,CAAC,EAAmC,CAAC,CAAC;QACjD,KAAK,CAAC,IAAI,CAAC,YAAY,EAAE,kBAAkB,CAAC,CAAC,QAAQ,EAAE,CAAC;QACxD,KAAK,CAAC,IAAI,CAAC,QAAQ,EAAE,0BAA0B,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;QAEhE,MAAM,aAAa,GAAuB;YACxC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,MAAM;SAChC,CAAC;QACF,KAAK,CAAC,IAAI,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC,QAAQ,CAAC;YAC5C,aAAa;YACb,sBAAsB,EAAE,EAAE;YAC1B,SAAS,EAAE,EAAE;YACb,KAAK,EAAE,EAAE;YACT,UAAU,EAAE,EAAE;SACkB,CAAC,CAAC;QACpC,MAAM,iBAAiB,GAAG,KAAK,CAAC,IAAI,CAAC,WAAW,EAAE,kBAAkB,CAAC,CAAC;QACtE,iBAAiB,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC;QAC1D,iBAAiB,CAAC,QAAQ,CAAC,iBAAiB,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;QAC/D,iBAAiB,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;QACpD,MAAM,iBAAiB,GAAG,KAAK,CAAC,IAAI,CAAC,WAAW,EAAE,kBAAkB,CAAC,CAAC;QACtE,iBAAiB,CAAC,QAAQ,CAAC,eAAe,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QAC5D,iBAAiB,CAAC,QAAQ,CAAC,cAAc,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;QAC5D,KAAK,CAAC,IAAI,CAAC,GAAG,EAAE,kBAAkB,CAAC,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAC;QAC5D,IAAA,gCAAgB,EAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACjC,IAAA,0CAA0B,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC;QAEpC,uEAAuE;QACvE,0EAA0E;QAC1E,iBAAiB;QACjB,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,GAAG,IAAI,CAAC;QACrC,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,GAAG,MAAM,CAAC;QAEnC,MAAM,eAAe,GAAG,KAAK,CAAC,IAAI,CAAC,OAAO,EAAE,aAAa,CAAC,CAAC;QAC3D,MAAM,cAAc,GAAG,KAAK,CAAC,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QACzD,iEAAiE;QACjE,MAAM,aAAa,GAAG,OAAO,CAAC,kBAAkB,CAAC,CAAC;QAElD,uEAAuE;QACvE,oEAAoE;QACpE,4EAA4E;QAC5E,wEAAwE;QACxE,MAAM,aAAa,CAAC,UAAU,CAAC;QAE/B,CAAC,CAAC,SAAS,CAAC,eAAe,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,cAAc,CAAC,CAAC;QAC/D,CAAC,CAAC,SAAS,CAAC,eAAe,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,YAAY,CAAC,CAAC;QAC7D,CAAC,CAAC,SAAS,CAAC,cAAc,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,cAAc,CAAC,CAAC;QAC9D,CAAC,CAAC,SAAS,CAAC,cAAc,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,YAAY,CAAC,CAAC;IAC9D,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}
\ No newline at end of file
+{"version":3,"file":"analyze-action-env.test.js","sourceRoot":"","sources":["../src/analyze-action-env.test.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAAA,8CAAuB;AACvB,6CAA+B;AAE/B,4DAA8C;AAC9C,mDAAqC;AACrC,kDAAoC;AACpC,4DAA8C;AAC9C,sDAAwC;AACxC,8DAAgD;AAChD,mDAIyB;AACzB,6CAA+B;AAE/B,IAAA,0BAAU,EAAC,aAAI,CAAC,CAAC;AAEjB,4EAA4E;AAC5E,4EAA4E;AAC5E,+EAA+E;AAC/E,+EAA+E;AAC/E,gFAAgF;AAChF,iCAAiC;AAEjC,IAAA,aAAI,EAAC,8DAA8D,EAAE,KAAK,EAAE,CAAC,EAAE,EAAE;IAC/E,MAAM,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,MAAM,EAAE,EAAE;QACrC,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,GAAG,IAAI,CAAC,iBAAiB,CAAC;QAC1D,OAAO,CAAC,GAAG,CAAC,mBAAmB,CAAC,GAAG,sCAAsC,CAAC;QAC1E,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,GAAG,wBAAwB,CAAC;QACzD,KAAK;aACF,IAAI,CAAC,YAAY,EAAE,wBAAwB,CAAC;aAC5C,QAAQ,CAAC,EAAmC,CAAC,CAAC;QACjD,KAAK,CAAC,IAAI,CAAC,YAAY,EAAE,kBAAkB,CAAC,CAAC,QAAQ,EAAE,CAAC;QACxD,KAAK,CAAC,IAAI,CAAC,QAAQ,EAAE,0BAA0B,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAC;QAEhE,MAAM,aAAa,GAAuB;YACxC,IAAI,EAAE,IAAI,CAAC,aAAa,CAAC,MAAM;SAChC,CAAC;QACF,KAAK,CAAC,IAAI,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC,QAAQ,CAAC;YAC5C,aAAa;YACb,sBAAsB,EAAE,EAAE;YAC1B,SAAS,EAAE,EAAE;YACb,KAAK,EAAE,EAAE;YACT,UAAU,EAAE,EAAE;SACkB,CAAC,CAAC;QACpC,MAAM,iBAAiB,GAAG,KAAK,CAAC,IAAI,CAAC,WAAW,EAAE,kBAAkB,CAAC,CAAC;QACtE,iBAAiB,CAAC,QAAQ,CAAC,OAAO,CAAC,CAAC,OAAO,CAAC,YAAY,CAAC,CAAC;QAC1D,iBAAiB,CAAC,QAAQ,CAAC,iBAAiB,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;QAC/D,iBAAiB,CAAC,QAAQ,CAAC,QAAQ,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC;QACpD,MAAM,iBAAiB,GAAG,KAAK,CAAC,IAAI,CAAC,WAAW,EAAE,kBAAkB,CAAC,CAAC;QACtE,iBAAiB,CAAC,QAAQ,CAAC,cAAc,CAAC,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;QAC5D,KAAK,CAAC,IAAI,CAAC,GAAG,EAAE,kBAAkB,CAAC,CAAC,QAAQ,CAAC,aAAa,CAAC,CAAC;QAC5D,IAAA,gCAAgB,EAAC,MAAM,EAAE,MAAM,CAAC,CAAC;QACjC,IAAA,0CAA0B,EAAC,GAAG,EAAE,EAAE,CAAC,CAAC;QAEpC,uEAAuE;QACvE,0EAA0E;QAC1E,iBAAiB;QACjB,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC,GAAG,IAAI,CAAC;QACrC,OAAO,CAAC,GAAG,CAAC,YAAY,CAAC,GAAG,MAAM,CAAC;QAEnC,MAAM,eAAe,GAAG,KAAK,CAAC,IAAI,CAAC,OAAO,EAAE,aAAa,CAAC,CAAC;QAC3D,MAAM,cAAc,GAAG,KAAK,CAAC,IAAI,CAAC,OAAO,EAAE,YAAY,CAAC,CAAC;QACzD,iEAAiE;QACjE,MAAM,aAAa,GAAG,OAAO,CAAC,kBAAkB,CAAC,CAAC;QAElD,uEAAuE;QACvE,oEAAoE;QACpE,4EAA4E;QAC5E,wEAAwE;QACxE,MAAM,aAAa,CAAC,UAAU,CAAC;QAE/B,CAAC,CAAC,SAAS,CAAC,eAAe,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,cAAc,CAAC,CAAC;QAC/D,CAAC,CAAC,SAAS,CAAC,eAAe,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,YAAY,CAAC,CAAC;QAC7D,CAAC,CAAC,SAAS,CAAC,cAAc,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,cAAc,CAAC,CAAC;QAC9D,CAAC,CAAC,SAAS,CAAC,cAAc,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,YAAY,CAAC,CAAC;IAC9D,CAAC,CAAC,CAAC;AACL,CAAC,CAAC,CAAC"}
\ No newline at end of file
diff --git a/lib/analyze-action-input.test.js b/lib/analyze-action-input.test.js
index e72ac09589..a0cc5c1798 100644
--- a/lib/analyze-action-input.test.js
+++ b/lib/analyze-action-input.test.js
@@ -77,7 +77,6 @@ const util = __importStar(require("./util"));
         requiredInputStub.withArgs("upload-database").returns("false");
         requiredInputStub.withArgs("output").returns("out");
         const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
-        optionalInputStub.withArgs("cleanup-level").returns("none");
         optionalInputStub.withArgs("expect-error").returns("false");
         sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
         sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
diff --git a/lib/analyze-action-input.test.js.map b/lib/analyze-action-input.test.js.map
index dfdec3e594..1e37d80e49 100644
--- a/lib/analyze-action-input.test.js.map
+++ b/lib/analyze-action-input.test.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/lib/analyze-action.js b/lib/analyze-action.js
index 5b58be97d5..d2d5beffff 100644
--- a/lib/analyze-action.js
+++ b/lib/analyze-action.js
@@ -202,14 +202,19 @@ async function run() {
         await (0, analyze_1.warnIfGoInstalledAfterInit)(config, logger);
         await runAutobuildIfLegacyGoWorkflow(config, logger);
         dbCreationTimings = await (0, analyze_1.runFinalize)(outputDir, threads, memory, codeql, config, logger);
+        if (actionsUtil.getOptionalInput("cleanup-level") !== "") {
+            logger.info("The 'cleanup-level' input is ignored since the CodeQL Action no longer writes intermediate results to the database. This input can safely be removed from your workflow.");
+        }
         // An overlay-base database should always use the 'overlay' cleanup level
         // to preserve the cached intermediate results.
         //
-        // Note that we may be overriding the 'cleanup-level' input parameter.
+        // Otherwise, use cleanup level 'none'. We are already discarding
+        // intermediate results during evaluation with '--expect-discarded-cache',
+        // so there is nothing to clean up.
         const cleanupLevel = config.augmentationProperties.overlayDatabaseMode ===
             overlay_database_utils_1.OverlayDatabaseMode.OverlayBase
             ? "overlay"
-            : actionsUtil.getOptionalInput("cleanup-level") || "brutal";
+            : "none";
         if (actionsUtil.getRequiredInput("skip-queries") !== "true") {
             runStats = await (0, analyze_1.runQueries)(outputDir, memory, util.getAddSnippetsFlag(actionsUtil.getRequiredInput("add-snippets")), threads, cleanupLevel, diffRangePackDir, actionsUtil.getOptionalInput("category"), config, logger, features);
         }
diff --git a/lib/analyze-action.js.map b/lib/analyze-action.js.map
index 5b4a8d9cf2..787e0a18e4 100644
--- a/lib/analyze-action.js.map
+++ b/lib/analyze-action.js.map
@@ -1 +1 @@
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\ No newline at end of file
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\ No newline at end of file
diff --git a/src/analyze-action-env.test.ts b/src/analyze-action-env.test.ts
index f0e15be44e..0f5a011bfd 100644
--- a/src/analyze-action-env.test.ts
+++ b/src/analyze-action-env.test.ts
@@ -49,7 +49,6 @@ test("analyze action with RAM & threads from environment variables", async (t) =
     requiredInputStub.withArgs("upload-database").returns("false");
     requiredInputStub.withArgs("output").returns("out");
     const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
-    optionalInputStub.withArgs("cleanup-level").returns("none");
     optionalInputStub.withArgs("expect-error").returns("false");
     sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
     setupActionsVars(tmpDir, tmpDir);
diff --git a/src/analyze-action-input.test.ts b/src/analyze-action-input.test.ts
index 5eeb9a262e..68487b42d9 100644
--- a/src/analyze-action-input.test.ts
+++ b/src/analyze-action-input.test.ts
@@ -47,7 +47,6 @@ test("analyze action with RAM & threads from action inputs", async (t) => {
     requiredInputStub.withArgs("upload-database").returns("false");
     requiredInputStub.withArgs("output").returns("out");
     const optionalInputStub = sinon.stub(actionsUtil, "getOptionalInput");
-    optionalInputStub.withArgs("cleanup-level").returns("none");
     optionalInputStub.withArgs("expect-error").returns("false");
     sinon.stub(api, "getGitHubVersion").resolves(gitHubVersion);
     sinon.stub(gitUtils, "isAnalyzingDefaultBranch").resolves(true);
diff --git a/src/analyze-action.ts b/src/analyze-action.ts
index 80ed43b21b..3e56e6aa22 100644
--- a/src/analyze-action.ts
+++ b/src/analyze-action.ts
@@ -295,15 +295,23 @@ async function run() {
       logger,
     );
 
+    if (actionsUtil.getOptionalInput("cleanup-level") !== "") {
+      logger.info(
+        "The 'cleanup-level' input is ignored since the CodeQL Action no longer writes intermediate results to the database. This input can safely be removed from your workflow.",
+      );
+    }
+
     // An overlay-base database should always use the 'overlay' cleanup level
     // to preserve the cached intermediate results.
     //
-    // Note that we may be overriding the 'cleanup-level' input parameter.
+    // Otherwise, use cleanup level 'none'. We are already discarding
+    // intermediate results during evaluation with '--expect-discarded-cache',
+    // so there is nothing to clean up.
     const cleanupLevel =
       config.augmentationProperties.overlayDatabaseMode ===
       OverlayDatabaseMode.OverlayBase
         ? "overlay"
-        : actionsUtil.getOptionalInput("cleanup-level") || "brutal";
+        : "none";
 
     if (actionsUtil.getRequiredInput("skip-queries") !== "true") {
       runStats = await runQueries(