diff --git a/.changeset/cold-lemons-design.md b/.changeset/cold-lemons-design.md
new file mode 100644
index 0000000000..9bdadac9c7
--- /dev/null
+++ b/.changeset/cold-lemons-design.md
@@ -0,0 +1,5 @@
+---
+'@backstage/plugin-app': patch
+---
+
+Log a warning when `SwappableComponent` extensions are installed outside of using the `app` plugin
diff --git a/plugins/app/src/apis/SwappableComponentsApi/DefaultSwappableComponentsApi.test.tsx b/plugins/app/src/apis/SwappableComponentsApi/DefaultSwappableComponentsApi.test.tsx
index 823d48e21c..07ef891926 100644
--- a/plugins/app/src/apis/SwappableComponentsApi/DefaultSwappableComponentsApi.test.tsx
+++ b/plugins/app/src/apis/SwappableComponentsApi/DefaultSwappableComponentsApi.test.tsx
@@ -17,6 +17,7 @@
 import {
   ApiBlueprint,
   createExtensionInput,
+  createFrontendModule,
   createSwappableComponent,
   SwappableComponentBlueprint,
   swappableComponentsApiRef,
@@ -202,7 +203,13 @@ describe('DefaultSwappableComponentsApi', () => {
         });
 
         renderInTestApp(<MockComponent />, {
-          extensions: [api, override],
+          extensions: [api],
+          features: [
+            createFrontendModule({
+              pluginId: 'app',
+              extensions: [override],
+            }),
+          ],
         });
 
         await expect(
@@ -225,7 +232,13 @@ describe('DefaultSwappableComponentsApi', () => {
         });
 
         renderInTestApp(<MockComponent />, {
-          extensions: [api, override],
+          extensions: [api],
+          features: [
+            createFrontendModule({
+              pluginId: 'app',
+              extensions: [override],
+            }),
+          ],
         });
 
         await expect(
@@ -252,7 +265,13 @@ describe('DefaultSwappableComponentsApi', () => {
         });
 
         renderInTestApp(<MockComponent external="test" />, {
-          extensions: [api, override],
+          extensions: [api],
+          features: [
+            createFrontendModule({
+              pluginId: 'app',
+              extensions: [override],
+            }),
+          ],
         });
 
         await expect(
diff --git a/plugins/app/src/extensions/SwappableComponentsApi.ts b/plugins/app/src/extensions/SwappableComponentsApi.ts
index ea57a6f487..f261d999c0 100644
--- a/plugins/app/src/extensions/SwappableComponentsApi.ts
+++ b/plugins/app/src/extensions/SwappableComponentsApi.ts
@@ -37,12 +37,30 @@ export const SwappableComponentsApi = ApiBlueprint.makeWithOverrides({
       defineParams({
         api: swappableComponentsApiRef,
         deps: {},
-        factory: () =>
-          DefaultSwappableComponentsApi.fromComponents(
-            inputs.components.map(i =>
+        factory: () => {
+          const nonAppExtensions = inputs.components.filter(
+            i => i.node.spec.plugin?.id !== 'app',
+          );
+
+          if (nonAppExtensions.length > 0) {
+            // eslint-disable-next-line no-console
+            console.warn(
+              `SwappableComponents should only be installed as an extension in the app plugin. You can either use appPlugin.override(), or provide a module for the app-plugin with the extension there instead. Invalid extensions: ${nonAppExtensions
+                .map(i => i.node.spec.id)
+                .join(', ')}`,
+            );
+          }
+
+          const appExtensions = inputs.components.filter(
+            i => i.node.spec.plugin?.id === 'app',
+          );
+
+          return DefaultSwappableComponentsApi.fromComponents(
+            appExtensions.map(i =>
               i.get(SwappableComponentBlueprint.dataRefs.component),
             ),
-          ),
+          );
+        },
       }),
     );
   },