diff --git a/.changeset/polite-shoes-allow.md b/.changeset/polite-shoes-allow.md
new file mode 100644
index 0000000000..b7e06bce6f
--- /dev/null
+++ b/.changeset/polite-shoes-allow.md
@@ -0,0 +1,5 @@
+---
+'@backstage/frontend-app-api': patch
+---
+
+Added the ability to ignore unknown extension config by passing `{ flags: { allowUnknownExtensionConfig: true } }` to `createSpecializedApp`.
diff --git a/packages/frontend-app-api/report.api.md b/packages/frontend-app-api/report.api.md
index f24d662df4..d2a3ac4d3b 100644
--- a/packages/frontend-app-api/report.api.md
+++ b/packages/frontend-app-api/report.api.md
@@ -34,6 +34,9 @@ export function createSpecializedApp(options?: {
   extensionFactoryMiddleware?:
     | ExtensionFactoryMiddleware
     | ExtensionFactoryMiddleware[];
+  flags?: {
+    allowUnknownExtensionConfig?: boolean;
+  };
 }): {
   apis: ApiHolder;
   tree: AppTree;
diff --git a/packages/frontend-app-api/src/tree/resolveAppNodeSpecs.ts b/packages/frontend-app-api/src/tree/resolveAppNodeSpecs.ts
index 0abbbb3560..3da68dcb50 100644
--- a/packages/frontend-app-api/src/tree/resolveAppNodeSpecs.ts
+++ b/packages/frontend-app-api/src/tree/resolveAppNodeSpecs.ts
@@ -33,12 +33,14 @@ export function resolveAppNodeSpecs(options: {
   builtinExtensions?: Extension<any, any>[];
   parameters?: Array<ExtensionParameters>;
   forbidden?: Set<string>;
+  allowUnknownExtensionConfig?: boolean;
 }): AppNodeSpec[] {
   const {
     builtinExtensions = [],
     parameters = [],
     forbidden = new Set(),
     features = [],
+    allowUnknownExtensionConfig = false,
   } = options;
 
   const plugins = features.filter(OpaqueFrontendPlugin.isType);
@@ -202,7 +204,7 @@ export function resolveAppNodeSpecs(options: {
         existing.params.disabled = Boolean(overrideParam.disabled);
       }
       order.set(extensionId, existing);
-    } else {
+    } else if (!allowUnknownExtensionConfig) {
       throw new Error(`Extension ${extensionId} does not exist`);
     }
   }
diff --git a/packages/frontend-app-api/src/wiring/createSpecializedApp.tsx b/packages/frontend-app-api/src/wiring/createSpecializedApp.tsx
index 1a4c7dbc78..5f6692d600 100644
--- a/packages/frontend-app-api/src/wiring/createSpecializedApp.tsx
+++ b/packages/frontend-app-api/src/wiring/createSpecializedApp.tsx
@@ -208,6 +208,7 @@ export function createSpecializedApp(options?: {
   extensionFactoryMiddleware?:
     | ExtensionFactoryMiddleware
     | ExtensionFactoryMiddleware[];
+  flags?: { allowUnknownExtensionConfig?: boolean };
 }): { apis: ApiHolder; tree: AppTree } {
   const config = options?.config ?? new ConfigReader({}, 'empty-config');
   const features = deduplicateFeatures(options?.features ?? []);
@@ -221,6 +222,7 @@ export function createSpecializedApp(options?: {
       ],
       parameters: readAppExtensionsConfig(config),
       forbidden: new Set(['root']),
+      allowUnknownExtensionConfig: options?.flags?.allowUnknownExtensionConfig,
     }),
   );