diff --git a/packages/cli/src/update.ts b/packages/cli/src/update.ts
index 0ce15e75..202f2e3e 100644
--- a/packages/cli/src/update.ts
+++ b/packages/cli/src/update.ts
@@ -554,6 +554,33 @@ function migrateImportedLayout(
  * migrations must preserve semantics and are protected by update backups.
  */
 
+/** Remove a `key: <scalar>` line from a config source, e.g. `compatibilityDate: "..."`. */
+function removeScalarConfigKey(source: string, key: string): string {
+  return source.replace(new RegExp(`^[ \\t]*${key}:.*\\n`, "m"), "");
+}
+
+/**
+ * Remove a `key: { ... }` object property from a config source, using balanced-brace
+ * scanning so a nested `{ ... }` inside the value can't truncate the removal early.
+ */
+function removeObjectConfigKey(source: string, key: string): string {
+  const match = new RegExp(`^[ \\t]*${key}\\s*:\\s*\\{`, "m").exec(source);
+  if (!match) return source;
+  const lineStart = match.index;
+  const openBrace = match.index + match[0].length - 1;
+  const closeBrace = findMatching(source, openBrace);
+  if (closeBrace < 0) return source;
+
+  let end = closeBrace + 1;
+  while (source[end] === " " || source[end] === "\t") end++;
+  if (source[end] === ",") end++;
+  while (source[end] === " " || source[end] === "\t") end++;
+  if (source[end] === "\r") end++;
+  if (source[end] === "\n") end++;
+
+  return source.slice(0, lineStart) + source.slice(end);
+}
+
 const MIGRATIONS: Migration[] = [
   {
     version: "0.8.0",
@@ -820,6 +847,27 @@ const MIGRATIONS: Migration[] = [
       // no application source rewrite is required.
     },
   },
+  {
+    version: "0.9.0",
+    id: "remove-dead-config-keys",
+    description: "Delete compatibilityDate, frameworkBehaviour, functions, and compatibility",
+    apply(ctx) {
+      const file = join(ctx.appRoot, "wrnexus.config.ts");
+      if (!existsSync(file)) return;
+
+      const before = readFileSync(file, "utf8");
+      let after = before;
+      after = removeScalarConfigKey(after, "compatibilityDate");
+      after = removeScalarConfigKey(after, "frameworkBehaviour");
+      after = removeObjectConfigKey(after, "functions");
+      after = removeObjectConfigKey(after, "compatibility");
+
+      if (after === before) return;
+
+      ctx.report.changedAutomatically.push(`${file}: removed dead compatibility keys`);
+      if (!ctx.dryRun) writeFileSync(file, after, "utf8");
+    },
+  },
 ];
 
 /** Release tooling uses this to require an explicit migration entry per version. */
diff --git a/packages/cli/test/migrate-config-keys.test.ts b/packages/cli/test/migrate-config-keys.test.ts
new file mode 100644
index 00000000..b834e940
--- /dev/null
+++ b/packages/cli/test/migrate-config-keys.test.ts
@@ -0,0 +1,92 @@
+import { afterEach, expect, test } from "bun:test";
+import { mkdirSync, mkdtempSync, readFileSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { updateApp } from "../src/update.ts";
+
+const roots: string[] = [];
+afterEach(() => {
+  for (const root of roots.splice(0)) rmSync(root, { recursive: true, force: true });
+});
+
+const CONFIG = `export default {
+  compatibilityDate: "2026-08-02",
+  frameworkBehaviour: 1,
+  functions: { legacyDefaultRuntime: "current" },
+  compatibility: { legacyEmit: false, stringLayouts: false },
+  observability: { sampleRate: 1 },
+};
+`;
+
+const NESTED_CONFIG = `export default {
+  compatibilityDate: "2026-08-02",
+  frameworkBehaviour: 1,
+  functions: { legacyDefaultRuntime: "current", overrides: { a: { b: 1 } } },
+  compatibility: { legacyEmit: false, nested: { deeper: { value: true } } },
+  observability: { sampleRate: 1 },
+};
+`;
+
+function project(config = CONFIG): string {
+  const root = mkdtempSync(join(tmpdir(), "wrnexus-migrate-"));
+  roots.push(root);
+  mkdirSync(join(root, "app"), { recursive: true });
+  writeFileSync(
+    join(root, "package.json"),
+    JSON.stringify({
+      name: "config-migrate-app",
+      dependencies: { "@wrnexus/core": "^0.8.0" },
+      wrnexus: { version: "0.8.0" },
+    }),
+  );
+  writeFileSync(join(root, "wrnexus.config.ts"), config);
+  return root;
+}
+
+test("the removed keys are deleted and the rest is kept", () => {
+  const root = project();
+  updateApp(root, "0.9.0", false);
+  const config = readFileSync(join(root, "wrnexus.config.ts"), "utf8");
+
+  expect(config).not.toContain("compatibilityDate");
+  expect(config).not.toContain("frameworkBehaviour");
+  expect(config).not.toContain("legacyDefaultRuntime");
+  expect(config).not.toContain("legacyEmit");
+  expect(config).toContain("observability");
+});
+
+test("running it twice changes nothing the second time", () => {
+  const root = project();
+  updateApp(root, "0.9.0", false);
+  const once = readFileSync(join(root, "wrnexus.config.ts"), "utf8");
+  updateApp(root, "0.9.0", false);
+
+  expect(readFileSync(join(root, "wrnexus.config.ts"), "utf8")).toBe(once);
+});
+
+test("a dry run writes nothing", () => {
+  const root = project();
+  updateApp(root, "0.9.0", true);
+
+  expect(readFileSync(join(root, "wrnexus.config.ts"), "utf8")).toBe(CONFIG);
+});
+
+test("a nested object value under a removed key does not corrupt the file", () => {
+  const root = project(NESTED_CONFIG);
+  updateApp(root, "0.9.0", false);
+  const config = readFileSync(join(root, "wrnexus.config.ts"), "utf8");
+
+  expect(config).not.toContain("compatibilityDate");
+  expect(config).not.toContain("frameworkBehaviour");
+  expect(config).not.toContain("legacyDefaultRuntime");
+  expect(config).not.toContain("legacyEmit");
+  expect(config).not.toContain("overrides");
+  expect(config).not.toContain("nested");
+  expect(config).toContain("observability");
+
+  // The file must remain valid, balanced TypeScript: an equal number of
+  // opening and closing braces, and it must still be parseable as a module.
+  const opens = (config.match(/\{/g) ?? []).length;
+  const closes = (config.match(/\}/g) ?? []).length;
+  expect(opens).toBe(closes);
+});