diff --git a/packages/app-defaults/src/defaults/apis.ts b/packages/app-defaults/src/defaults/apis.ts
index c53ce63ada..7ff8ce16bc 100644
--- a/packages/app-defaults/src/defaults/apis.ts
+++ b/packages/app-defaults/src/defaults/apis.ts
@@ -65,17 +65,9 @@ export const apis = [
     api: discoveryApiRef,
     deps: { configApi: configApiRef },
     factory: ({ configApi }) => {
-      let baseUrl;
-      try {
-        // Try parsing the url relative to the current document origin, if it fails the URL is misformed.
-        baseUrl = new URL(
-          configApi.getString('backend.baseUrl'),
-          document.location.origin,
-        ).href.replace(/\/$/, '');
-      } catch (err) {
-        baseUrl = configApi.getString('backend.baseUrl');
-      }
-      return UrlPatternDiscovery.compile(`${baseUrl}/api/{{ pluginId }}`);
+      return UrlPatternDiscovery.compile(
+        `${configApi.getString('backend.baseUrl')}/api/{{ pluginId }}`,
+      );
     },
   }),
   createApiFactory({
diff --git a/packages/core-app-api/src/app/AppManager.test.tsx b/packages/core-app-api/src/app/AppManager.test.tsx
index c70b43581a..33b7ad5b9a 100644
--- a/packages/core-app-api/src/app/AppManager.test.tsx
+++ b/packages/core-app-api/src/app/AppManager.test.tsx
@@ -34,6 +34,7 @@ import {
   createSubRouteRef,
   createRoutableExtension,
   analyticsApiRef,
+  useApiHolder,
 } from '@backstage/core-plugin-api';
 import { AppManager } from './AppManager';
 import { AppComponents, AppIcons } from './types';
@@ -569,4 +570,93 @@ describe('Integration Test', () => {
       ),
     ]);
   });
+
+  it('should add the fully qualified origin when the backend.baseUrl is relative', async () => {
+    const app = new AppManager({
+      apis: [],
+      defaultApis: [],
+      themes: [
+        {
+          id: 'light',
+          title: 'Light Theme',
+          variant: 'light',
+          Provider: ({ children }) => <>{children}</>,
+        },
+      ],
+      icons,
+      plugins: [],
+      components,
+      configLoader: async () => [
+        {
+          context: 'test',
+          data: {
+            backend: {
+              baseUrl: '/',
+            },
+          },
+        },
+      ],
+    });
+
+    const Provider = app.getProvider();
+    const ConfigDisplay = () => {
+      const apiHolder = useApiHolder();
+      const config = apiHolder.get(configApiRef);
+      return <span>{config?.getString('backend.baseUrl')}</span>;
+    };
+
+    const dom = await renderWithEffects(
+      <Provider>
+        <ConfigDisplay />
+      </Provider>,
+    );
+
+    // Verify that the backend.baseUrl is set correctly by the AppManager.
+    expect(dom.getByText(document.location.origin)).toBeTruthy();
+  });
+
+  it('should NOT change the origin when the backend.baseUrl is absolute', async () => {
+    const backendUrl = 'http://localhost:7007';
+    const app = new AppManager({
+      apis: [],
+      defaultApis: [],
+      themes: [
+        {
+          id: 'light',
+          title: 'Light Theme',
+          variant: 'light',
+          Provider: ({ children }) => <>{children}</>,
+        },
+      ],
+      icons,
+      plugins: [],
+      components,
+      configLoader: async () => [
+        {
+          context: 'test',
+          data: {
+            backend: {
+              baseUrl: backendUrl,
+            },
+          },
+        },
+      ],
+    });
+
+    const Provider = app.getProvider();
+    const ConfigDisplay = () => {
+      const apiHolder = useApiHolder();
+      const config = apiHolder.get(configApiRef);
+      return <span>{config?.getString('backend.baseUrl')}</span>;
+    };
+
+    const dom = await renderWithEffects(
+      <Provider>
+        <ConfigDisplay />
+      </Provider>,
+    );
+
+    // Verify that the backend.baseUrl is set correctly by the AppManager.
+    expect(dom.getByText(backendUrl)).toBeTruthy();
+  });
 });
diff --git a/packages/core-app-api/src/app/AppManager.tsx b/packages/core-app-api/src/app/AppManager.tsx
index bbd27f84ce..cd571c7799 100644
--- a/packages/core-app-api/src/app/AppManager.tsx
+++ b/packages/core-app-api/src/app/AppManager.tsx
@@ -154,7 +154,34 @@ function useConfigLoader(
     };
   }
 
-  const configReader = ConfigReader.fromConfigs(config.value ?? []);
+  let configReader = ConfigReader.fromConfigs(config.value ?? []);
+
+  const getFullBackendUrl = () => {
+    // Backend.baseUrl should always be defined.
+    let url;
+    try {
+      url = new URL(
+        configReader.getString('backend.baseUrl'),
+        document.location.origin,
+      ).href.replace(/\/$/, '');
+    } catch (err) {
+      // Backend.baseUrl was not a valid URL. This should be caught during the build process.
+    }
+    return url;
+  };
+
+  const relativeBackendConfig = {
+    data: {
+      backend: {
+        baseUrl: getFullBackendUrl(),
+      },
+    },
+    context: 'relative-override',
+  };
+
+  configReader = ConfigReader.fromConfigs(
+    config.value ? [...config.value, relativeBackendConfig] : [],
+  );
 
   return { api: configReader };
 }