diff --git a/packages/frontend-app-api/src/wiring/parameters.ts b/packages/frontend-app-api/src/wiring/parameters.ts
index 1b2831aaca..acde9d9ec0 100644
--- a/packages/frontend-app-api/src/wiring/parameters.ts
+++ b/packages/frontend-app-api/src/wiring/parameters.ts
@@ -188,6 +188,14 @@ export interface ExtensionInstanceParameters {
   config?: unknown;
 }
 
+function preventRootExtensionOverride(id: string) {
+  if (id === 'root') {
+    throw new Error(
+      'There is a root extension in the app config file and root extensions are not configurable',
+    );
+  }
+}
+
 /** @internal */
 export function mergeExtensionParameters(options: {
   sources: BackstagePlugin[];
@@ -220,8 +228,10 @@ export function mergeExtensionParameters(options: {
   ];
 
   for (const overrideParam of parameters) {
+    const extensionId = overrideParam.id;
+    preventRootExtensionOverride(extensionId);
     const existingIndex = overrides.findIndex(
-      e => e.extension.id === overrideParam.id,
+      e => e.extension.id === extensionId,
     );
     if (existingIndex !== -1) {
       const existing = overrides[existingIndex];
@@ -243,7 +253,7 @@ export function mergeExtensionParameters(options: {
         }
       }
     } else {
-      throw new Error(`Extension ${overrideParam.id} does not exist`);
+      throw new Error(`Extension ${extensionId} does not exist`);
     }
   }