diff --git a/apps/example/nitro.config.ts b/apps/example/nitro.config.ts
index 527fd6f4..4352440b 100644
--- a/apps/example/nitro.config.ts
+++ b/apps/example/nitro.config.ts
@@ -6,7 +6,9 @@ export default defineConfig({
   preset: "vercel",
   modules: [
     juniorNitro({
-      pluginPackages: examplePluginPackages,
+      plugins: {
+        packages: examplePluginPackages,
+      },
     }),
   ],
   routes: {
diff --git a/apps/example/server.ts b/apps/example/server.ts
index cff16907..d9e5f548 100644
--- a/apps/example/server.ts
+++ b/apps/example/server.ts
@@ -5,7 +5,9 @@ import { examplePluginPackages } from "./plugin-packages";
 initSentry();
 
 const app = await createApp({
-  pluginPackages: examplePluginPackages,
+  plugins: {
+    packages: examplePluginPackages,
+  },
   configDefaults: {
     "sentry.org": "sentry",
   },
diff --git a/packages/junior/src/cli/check.ts b/packages/junior/src/cli/check.ts
index 1a64f73a..dbdf82c3 100644
--- a/packages/junior/src/cli/check.ts
+++ b/packages/junior/src/cli/check.ts
@@ -555,6 +555,46 @@ interface AppFileValidationResult {
   warnings: string[];
 }
 
+async function validateAppSourceFiles(
+  rootDir: string,
+  registeredConfigKeys: Set<string>,
+): Promise<AppFileValidationResult> {
+  const errors: string[] = [];
+  const warnings: string[] = [];
+
+  for (const fileName of ["server.ts", "server.js", "nitro.config.ts"]) {
+    const sourcePath = path.join(rootDir, fileName);
+    let source: string;
+    try {
+      source = await fs.readFile(sourcePath, "utf8");
+    } catch {
+      continue;
+    }
+
+    if (/\bpluginPackages\s*:/.test(source)) {
+      errors.push(
+        `${sourcePath}: pluginPackages is no longer supported. Use plugins: { packages: [...] }.`,
+      );
+    }
+
+    for (const defaultsBlock of source.matchAll(
+      /\bconfigDefaults\s*:\s*\{([\s\S]*?)\}/g,
+    )) {
+      const block = defaultsBlock[1] ?? "";
+      for (const keyMatch of block.matchAll(/["']([^"']+)["']\s*:/g)) {
+        const key = keyMatch[1];
+        if (key && !registeredConfigKeys.has(key)) {
+          errors.push(
+            `${sourcePath}: configDefaults key "${key}" is not a registered plugin config key`,
+          );
+        }
+      }
+    }
+  }
+
+  return { errors, warnings };
+}
+
 async function validateAppFiles(
   appDir: string,
 ): Promise<AppFileValidationResult> {
@@ -699,6 +739,16 @@ export async function runCheck(
     errors.push(...result.errors);
   }
 
+  const registeredConfigKeys = new Set(
+    pluginResults.flatMap((result) => result.manifest?.configKeys ?? []),
+  );
+  const appSourceResult = await validateAppSourceFiles(
+    resolvedRoot,
+    registeredConfigKeys,
+  );
+  warnings.push(...appSourceResult.warnings);
+  errors.push(...appSourceResult.errors);
+
   for (const skillDir of appAndLocalPluginSkillDirs) {
     const result = await validateSkillDirectory(skillDir, duplicateSkillNames);
     skillResultsByDir.set(skillDir, result);
diff --git a/packages/junior/tests/unit/cli/check-cli.test.ts b/packages/junior/tests/unit/cli/check-cli.test.ts
index 89b230dc..1d88e3a9 100644
--- a/packages/junior/tests/unit/cli/check-cli.test.ts
+++ b/packages/junior/tests/unit/cli/check-cli.test.ts
@@ -183,6 +183,108 @@ describe("check cli", () => {
     ]);
   });
 
+  it("fails when app source uses the removed pluginPackages option", async () => {
+    const repoRoot = makeTempDir("junior-validate-plugin-packages-option-");
+    writeFile(
+      path.join(repoRoot, "server.ts"),
+      [
+        'import { createApp } from "@sentry/junior";',
+        "",
+        "export default await createApp({",
+        '  pluginPackages: ["@acme/junior-demo"],',
+        "});",
+        "",
+      ].join("\n"),
+    );
+
+    const lines: string[] = [];
+    await expect(
+      runCheck(repoRoot, {
+        info: (line) => lines.push(line),
+        warn: (line) => lines.push(line),
+        error: (line) => lines.push(line),
+      }),
+    ).rejects.toThrow(
+      "Validation failed (1 error, 0 plugin manifests, 0 skill directories checked).",
+    );
+
+    expect(
+      lines.some((line) =>
+        line.includes(
+          "pluginPackages is no longer supported. Use plugins: { packages: [...] }.",
+        ),
+      ),
+    ).toBe(true);
+  });
+
+  it("fails when app configDefaults references an unregistered plugin key", async () => {
+    const repoRoot = makeTempDir("junior-validate-config-defaults-");
+    writeFile(
+      path.join(repoRoot, "package.json"),
+      JSON.stringify(
+        {
+          dependencies: {
+            "@acme/junior-demo": "1.0.0",
+          },
+        },
+        null,
+        2,
+      ),
+    );
+    const packageRoot = path.join(
+      repoRoot,
+      "node_modules",
+      "@acme",
+      "junior-demo",
+    );
+    writeFile(
+      path.join(packageRoot, "package.json"),
+      JSON.stringify({ name: "@acme/junior-demo", version: "1.0.0" }),
+    );
+    writeFile(
+      path.join(packageRoot, "plugin.yaml"),
+      [
+        "name: demo",
+        "description: Demo packaged plugin",
+        "config-keys:",
+        "  - org",
+        "",
+      ].join("\n"),
+    );
+    writeFile(
+      path.join(repoRoot, "server.ts"),
+      [
+        'import { createApp } from "@sentry/junior";',
+        "",
+        "export default await createApp({",
+        "  configDefaults: {",
+        '    "sentry.org": "sentry",',
+        "  },",
+        "});",
+        "",
+      ].join("\n"),
+    );
+
+    const lines: string[] = [];
+    await expect(
+      runCheck(repoRoot, {
+        info: (line) => lines.push(line),
+        warn: (line) => lines.push(line),
+        error: (line) => lines.push(line),
+      }),
+    ).rejects.toThrow(
+      "Validation failed (1 error, 1 plugin manifest, 0 skill directories checked).",
+    );
+
+    expect(
+      lines.some((line) =>
+        line.includes(
+          'configDefaults key "sentry.org" is not a registered plugin config key',
+        ),
+      ),
+    ).toBe(true);
+  });
+
   it("warns when official plugin package versions differ from core", async () => {
     const repoRoot = makeTempDir("junior-validate-version-skew-");
     writeFile(