diff --git a/src/core/public/application/application_service.test.ts b/src/core/public/application/application_service.test.ts
index 3ed164088bf5c7..de9e4d4496f3b2 100644
--- a/src/core/public/application/application_service.test.ts
+++ b/src/core/public/application/application_service.test.ts
@@ -15,13 +15,13 @@ import {
 import { createElement } from 'react';
 import { BehaviorSubject, Subject } from 'rxjs';
 import { bufferCount, take, takeUntil } from 'rxjs/operators';
-import { shallow, mount } from 'enzyme';
+import { mount, shallow } from 'enzyme';
 
 import { httpServiceMock } from '../http/http_service.mock';
 import { overlayServiceMock } from '../overlays/overlay_service.mock';
 import { MockLifecycle } from './test_types';
 import { ApplicationService } from './application_service';
-import { App, PublicAppInfo, AppNavLinkStatus, AppStatus, AppUpdater } from './types';
+import { App, AppDeepLink, AppNavLinkStatus, AppStatus, AppUpdater, PublicAppInfo } from './types';
 import { act } from 'react-dom/test-utils';
 
 const createApp = (props: Partial<App>): App => {
@@ -365,6 +365,85 @@ describe('#setup()', () => {
       expect(MockHistory.push).toHaveBeenCalledWith('/app/app1', undefined);
       MockHistory.push.mockClear();
     });
+
+    it('preserves the deep links if the update does not modify them', async () => {
+      const setup = service.setup(setupDeps);
+
+      const pluginId = Symbol('plugin');
+      const updater$ = new BehaviorSubject<AppUpdater>((app) => ({}));
+
+      const deepLinks: AppDeepLink[] = [
+        {
+          id: 'foo',
+          title: 'Foo',
+          searchable: true,
+          navLinkStatus: AppNavLinkStatus.visible,
+          path: '/foo',
+        },
+        {
+          id: 'bar',
+          title: 'Bar',
+          searchable: false,
+          navLinkStatus: AppNavLinkStatus.hidden,
+          path: '/bar',
+        },
+      ];
+
+      setup.register(pluginId, createApp({ id: 'app1', deepLinks, updater$ }));
+
+      const { applications$ } = await service.start(startDeps);
+
+      updater$.next((app) => ({ defaultPath: '/foo' }));
+
+      let appInfos = await applications$.pipe(take(1)).toPromise();
+
+      expect(appInfos.get('app1')!.deepLinks).toEqual([
+        {
+          deepLinks: [],
+          id: 'foo',
+          keywords: [],
+          navLinkStatus: 1,
+          path: '/foo',
+          searchable: true,
+          title: 'Foo',
+        },
+        {
+          deepLinks: [],
+          id: 'bar',
+          keywords: [],
+          navLinkStatus: 3,
+          path: '/bar',
+          searchable: false,
+          title: 'Bar',
+        },
+      ]);
+
+      updater$.next((app) => ({
+        deepLinks: [
+          {
+            id: 'bar',
+            title: 'Bar',
+            searchable: false,
+            navLinkStatus: AppNavLinkStatus.hidden,
+            path: '/bar',
+          },
+        ],
+      }));
+
+      appInfos = await applications$.pipe(take(1)).toPromise();
+
+      expect(appInfos.get('app1')!.deepLinks).toEqual([
+        {
+          deepLinks: [],
+          id: 'bar',
+          keywords: [],
+          navLinkStatus: 3,
+          path: '/bar',
+          searchable: false,
+          title: 'Bar',
+        },
+      ]);
+    });
   });
 });
 
diff --git a/src/core/public/application/application_service.tsx b/src/core/public/application/application_service.tsx
index 8c6090caabce19..2e804bf2f5413c 100644
--- a/src/core/public/application/application_service.tsx
+++ b/src/core/public/application/application_service.tsx
@@ -54,6 +54,7 @@ function filterAvailable<T>(m: Map<string, T>, capabilities: Capabilities) {
     )
   );
 }
+
 const findMounter = (mounters: Map<string, Mounter>, appRoute?: string) =>
   [...mounters].find(([, mounter]) => mounter.appRoute === appRoute);
 
@@ -414,13 +415,11 @@ const updateStatus = (app: App, statusUpdaters: AppUpdaterWrapper[]): App => {
           changes.navLinkStatus ?? AppNavLinkStatus.default,
           fields.navLinkStatus ?? AppNavLinkStatus.default
         ),
-        // deepLinks take the last defined update
-        deepLinks: fields.deepLinks
-          ? populateDeepLinkDefaults(fields.deepLinks)
-          : changes.deepLinks,
+        ...(fields.deepLinks ? { deepLinks: populateDeepLinkDefaults(fields.deepLinks) } : {}),
       };
     }
   });
+
   return {
     ...app,
     ...changes,