diff --git a/packages/firebase_core/firebase_core_web/lib/src/firebase_core_web.dart b/packages/firebase_core/firebase_core_web/lib/src/firebase_core_web.dart
index 192e673e7bd0..c1c83936a222 100644
--- a/packages/firebase_core/firebase_core_web/lib/src/firebase_core_web.dart
+++ b/packages/firebase_core/firebase_core_web/lib/src/firebase_core_web.dart
@@ -57,6 +57,14 @@ class FirebaseCoreWeb extends FirebasePlatform {
     );
   }
 
+  /// Whether [service] is still registered for per-app initialization.
+  ///
+  /// Used by tests to ensure App Check is not removed after the first
+  /// [initializeApp] (secondary apps must re-run ensurePluginInitialized).
+  @visibleForTesting
+  static bool isServiceRegistered(String service) =>
+      _services.containsKey(service);
+
   static const String _libraryName = 'flutter-fire-core';
 
   /// Registers that [FirebaseCoreWeb] is the platform implementation.
@@ -394,15 +402,20 @@ class FirebaseCoreWeb extends FirebasePlatform {
       }
     }
 
-    final appCheck = _services.remove('app-check');
-    if (appCheck != null) {
-      // Activate app check first
-      await appCheck.ensurePluginInitialized!(app!);
+    // Activate App Check before other services so Auth/etc. attach tokens.
+    // Do NOT remove 'app-check' from [_services]: secondary (named) apps also
+    // need ensurePluginInitialized on each Firebase.initializeApp() call.
+    // Removing it caused App Check to skip reactivation for named apps on
+    // reload, so accounts:lookup ran without X-Firebase-AppCheck (#18556).
+    final appCheck = _services['app-check'];
+    final appCheckEnsureInitialized = appCheck?.ensurePluginInitialized;
+    if (appCheckEnsureInitialized != null) {
+      await appCheckEnsureInitialized(app!);
     }
 
     await Future.wait(
-      _services.values.map((service) {
-        final ensureInitializedFunction = service.ensurePluginInitialized;
+      _services.entries.where((entry) => entry.key != 'app-check').map((entry) {
+        final ensureInitializedFunction = entry.value.ensurePluginInitialized;
 
         if (ensureInitializedFunction == null || app == null) {
           return Future.value();
diff --git a/packages/firebase_core/firebase_core_web/test/firebase_core_web_app_check_multi_app_test.dart b/packages/firebase_core/firebase_core_web/test/firebase_core_web_app_check_multi_app_test.dart
new file mode 100644
index 000000000000..88bfad5eb7a1
--- /dev/null
+++ b/packages/firebase_core/firebase_core_web/test/firebase_core_web_app_check_multi_app_test.dart
@@ -0,0 +1,67 @@
+// Copyright 2026 The Chromium Authors. All rights reserved.
+// Use of this source code is governed by a BSD-style license that can be
+// found in the LICENSE file.
+
+@TestOn('browser')
+library;
+
+import 'package:firebase_core_platform_interface/firebase_core_platform_interface.dart';
+import 'package:firebase_core_web/firebase_core_web.dart';
+import 'package:flutter_test/flutter_test.dart';
+
+void main() {
+  group('App Check multi-app initialization', () {
+    setUp(() async {
+      FirebasePlatform.instance = FirebaseCoreWeb();
+    });
+
+    test(
+      'keeps app-check registered and re-runs ensurePluginInitialized for named apps',
+      () async {
+        final initializedAppNames = <String>[];
+
+        FirebaseCoreWeb.registerService(
+          'app-check',
+          productNameOverride: 'app_check',
+          ensurePluginInitialized: (firebaseApp) async {
+            initializedAppNames.add(firebaseApp.name);
+          },
+        );
+
+        expect(FirebaseCoreWeb.isServiceRegistered('app-check'), isTrue);
+
+        const options = FirebaseOptions(
+          apiKey: 'fake-api-key',
+          appId: '1:1234567890:web:fake',
+          messagingSenderId: '1234567890',
+          projectId: 'fake-project',
+          authDomain: 'fake-project.firebaseapp.com',
+        );
+
+        final coreWeb = FirebaseCoreWeb();
+        final version = coreWeb.firebaseSDKVersion;
+        await coreWeb.injectSrcScript(
+          'https://www.gstatic.com/firebasejs/$version/firebase-app.js',
+          'firebase_core',
+        );
+
+        await FirebasePlatform.instance.initializeApp(options: options);
+
+        // Must still be registered so a secondary app can reactivate App Check.
+        expect(FirebaseCoreWeb.isServiceRegistered('app-check'), isTrue);
+        expect(initializedAppNames, contains('[DEFAULT]'));
+
+        await FirebasePlatform.instance.initializeApp(
+          name: 'prod',
+          options: options,
+        );
+
+        expect(FirebaseCoreWeb.isServiceRegistered('app-check'), isTrue);
+        expect(
+          initializedAppNames,
+          containsAll(['[DEFAULT]', 'prod']),
+        );
+      },
+    );
+  });
+}