diff --git a/packages/aws-cdk/lib/cli/cdk-toolkit.ts b/packages/aws-cdk/lib/cli/cdk-toolkit.ts
index 6a35c83b3..9f1e88eef 100644
--- a/packages/aws-cdk/lib/cli/cdk-toolkit.ts
+++ b/packages/aws-cdk/lib/cli/cdk-toolkit.ts
@@ -2113,11 +2113,29 @@ async function askUserConfirmation(
   });
 }
 
+/**
+ * Display a warning if there are flags that are different from the recommended value
+ *
+ * This happens if both of the following are true:
+ *
+ * - The user didn't configure the value
+ * - The default value for the flag (unconfiguredBehavesLike) is different from the recommended value
+ */
 export async function displayFlagsMessage(ioHost: IoHelper, toolkit: InternalToolkit, cloudExecutable: CloudExecutable): Promise<void> {
-  let numUnconfigured = (await toolkit.flags(cloudExecutable))
+  const flags = await toolkit.flags(cloudExecutable);
+
+  // The "unconfiguredBehavesLike" information got added later. If none of the flags have this information,
+  // we don't have enough information to reliably display this information without scaring users, so don't do anything.
+  if (flags.every(flag => flag.unconfiguredBehavesLike === undefined)) {
+    return;
+  }
+
+  const unconfiguredFlags = flags
     .filter(flag => !OBSOLETE_FLAGS.includes(flag.name))
-    .filter(flag => flag.userValue === undefined).length;
+    .filter(flag => (flag.unconfiguredBehavesLike?.v2 ?? false) !== flag.recommendedValue)
+    .filter(flag => flag.userValue === undefined);
 
+  const numUnconfigured = unconfiguredFlags.length;
   if (numUnconfigured > 0) {
     await ioHost.defaults.warn(`${numUnconfigured} feature flags are not configured. Run 'cdk --unstable=flags flags' to learn more.`);
   }