diff --git a/cli/src/__tests__/managed-install-check.test.ts b/cli/src/__tests__/managed-install-check.test.ts
index 354f0be7033..379fba77314 100644
--- a/cli/src/__tests__/managed-install-check.test.ts
+++ b/cli/src/__tests__/managed-install-check.test.ts
@@ -4,6 +4,7 @@ import path from "node:path";
 import { afterEach, describe, expect, it } from "vitest";
 import { managedInstallChecks } from "../checks/managed-install-check.js";
 import {
+  MANAGED_STORE_MARKER,
   buildNextManifest,
   flipCurrentAtomic,
   resolveInstallStorePaths,
@@ -51,9 +52,24 @@ describe("managed install doctor checks", () => {
       homeDir: root,
     });
     fs.mkdirSync(paths.cliRoot, { recursive: true });
+    fs.writeFileSync(paths.markerPath, MANAGED_STORE_MARKER);
 
     expect(managedInstallChecks(paths)).toEqual([
       expect.objectContaining({ name: "Managed install manifest", status: "fail" }),
     ]);
   });
+
+  it("ignores the shared CLI directory when it only contains update notice state", () => {
+    const root = fs.mkdtempSync(path.join(os.tmpdir(), "paperclip-install-doctor-"));
+    const paths = resolveInstallStorePaths({
+      paperclipHome: path.join(root, ".paperclip"),
+      homeDir: root,
+    });
+    fs.mkdirSync(paths.cliRoot, { recursive: true });
+    fs.writeFileSync(path.join(paths.cliRoot, "update-check.json"), "{}\n");
+
+    expect(managedInstallChecks(paths)).toEqual([
+      expect.objectContaining({ name: "Managed install", status: "pass" }),
+    ]);
+  });
 });
diff --git a/cli/src/checks/managed-install-check.ts b/cli/src/checks/managed-install-check.ts
index 324c5be812a..141b6ebadec 100644
--- a/cli/src/checks/managed-install-check.ts
+++ b/cli/src/checks/managed-install-check.ts
@@ -17,9 +17,13 @@ function pathContains(directory: string): boolean {
 }
 
 function hasManagedArtifacts(paths: InstallStorePaths): boolean {
-  return [paths.cliRoot, paths.manifestPath, paths.currentPath, paths.shimPath].some((entry) =>
-    fs.existsSync(entry),
-  );
+  return [
+    paths.installsRoot,
+    paths.manifestPath,
+    paths.markerPath,
+    paths.currentPath,
+    paths.shimPath,
+  ].some((entry) => fs.existsSync(entry));
 }
 
 export function nodeRuntimeCheck(): CheckResult {