diff --git a/.changeset/prepare-specialized-app-signin-flow.md b/.changeset/prepare-specialized-app-signin-flow.md
index 1ee2dba443..b8a7e65a06 100644
--- a/.changeset/prepare-specialized-app-signin-flow.md
+++ b/.changeset/prepare-specialized-app-signin-flow.md
@@ -3,4 +3,4 @@
 '@backstage/frontend-defaults': patch
 ---
 
-Adds `prepareSpecializedApp` as a new two-phase app wiring API for rendering a bootstrap tree before full app finalization. The bootstrap phase is exposed as a partial app tree through `getBootstrapApp()`, while `onFinalized()` provides a one-way handoff to the finalized app once bootstrap completes. The opaque reusable `sessionState` is returned from the finalized app and can be passed into a future `prepareSpecializedApp` call to skip sign-in and reuse the prepared session. The existing `createSpecializedApp` API is now deprecated and backed by `prepareSpecializedApp().finalize()`, while `createApp` has been updated to use the same prepare/finalize flow.
+Adds `prepareSpecializedApp` as a new two-phase app wiring API for rendering a bootstrap tree before full app finalization. The bootstrap phase is exposed as a partial app tree through `getBootstrapApp()`, while `onFinalized()` provides a one-way handoff to the finalized app once bootstrap completes. The opaque reusable `sessionState` is returned from the finalized app and can be passed into a future `prepareSpecializedApp` call to skip sign-in and reuse the prepared session. Conditional `app/root.elements` and predicate-gated APIs are now deferred until finalization, while unsupported bootstrap-visible predicates are downgraded to warnings and bootstrap extensions now surface warnings if they accessed APIs that only became available after finalization. The existing `createSpecializedApp` API is now deprecated and backed by `prepareSpecializedApp().finalize()`, while `createApp` has been updated to use the same prepare/finalize flow.
diff --git a/packages/frontend-app-api/src/tree/instantiateAppNodeTree.ts b/packages/frontend-app-api/src/tree/instantiateAppNodeTree.ts
index 5c9062dd06..23df618350 100644
--- a/packages/frontend-app-api/src/tree/instantiateAppNodeTree.ts
+++ b/packages/frontend-app-api/src/tree/instantiateAppNodeTree.ts
@@ -338,12 +338,28 @@ export function createAppNodeInstance(options: {
   apis: ApiHolder;
   attachments: ReadonlyMap<string, AppNode[]>;
   collector: ErrorCollector;
+  onMissingApi?(ctx: { node: AppNode; apiRefId: string }): void;
 }): AppNodeInstance | undefined {
   const { node, apis, attachments } = options;
   const collector = options.collector.child({ node });
   const { id, extension, config } = node.spec;
   const extensionData = new Map<string, unknown>();
   const extensionDataRefs = new Set<ExtensionDataRef<unknown>>();
+  const scopedApis: ApiHolder =
+    options.onMissingApi === undefined
+      ? apis
+      : {
+          get(apiRef) {
+            const api = apis.get(apiRef);
+            if (api === undefined) {
+              options.onMissingApi?.({
+                node,
+                apiRefId: apiRef.id,
+              });
+            }
+            return api;
+          },
+        };
 
   let parsedConfig: { [x: string]: any };
   try {
@@ -368,7 +384,7 @@ export function createAppNodeInstance(options: {
     if (internalExtension.version === 'v1') {
       const namedOutputs = internalExtension.factory({
         node,
-        apis,
+        apis: scopedApis,
         config: parsedConfig,
         inputs: resolveV1Inputs(internalExtension.inputs, attachments),
       });
@@ -389,7 +405,7 @@ export function createAppNodeInstance(options: {
     } else if (internalExtension.version === 'v2') {
       const context = {
         node,
-        apis,
+        apis: scopedApis,
         config: parsedConfig,
         inputs: resolveV2Inputs(
           internalExtension.inputs,
@@ -513,16 +529,26 @@ export function instantiateAppNodeTree(
   optionsOrPredicateContext?:
     | {
         stopAtAttachment?(ctx: { node: AppNode; input: string }): boolean;
+        skipChild?(ctx: {
+          node: AppNode;
+          input: string;
+          child: AppNode;
+        }): boolean;
+        onMissingApi?(ctx: { node: AppNode; apiRefId: string }): void;
         predicateContext?: Record<string, unknown>;
       }
     | Record<string, unknown>,
 ): boolean {
   const options: {
     stopAtAttachment?(ctx: { node: AppNode; input: string }): boolean;
+    skipChild?(ctx: { node: AppNode; input: string; child: AppNode }): boolean;
+    onMissingApi?(ctx: { node: AppNode; apiRefId: string }): void;
     predicateContext?: Record<string, unknown>;
   } =
     optionsOrPredicateContext &&
     ('stopAtAttachment' in optionsOrPredicateContext ||
+      'skipChild' in optionsOrPredicateContext ||
+      'onMissingApi' in optionsOrPredicateContext ||
       'predicateContext' in optionsOrPredicateContext)
       ? optionsOrPredicateContext
       : {
@@ -551,6 +577,9 @@ export function instantiateAppNodeTree(
         continue;
       }
       const instantiatedChildren = children.flatMap(child => {
+        if (options?.skipChild?.({ node, input, child })) {
+          return [];
+        }
         const childInstance = createInstance(child);
         if (!childInstance) {
           return [];
@@ -568,6 +597,7 @@ export function instantiateAppNodeTree(
       apis,
       attachments: instantiatedAttachments,
       collector,
+      onMissingApi: options?.onMissingApi,
     });
 
     return node.instance;
diff --git a/packages/frontend-app-api/src/wiring/FrontendApiRegistry.ts b/packages/frontend-app-api/src/wiring/FrontendApiRegistry.ts
index 1705aa9b25..8e56fe1ce8 100644
--- a/packages/frontend-app-api/src/wiring/FrontendApiRegistry.ts
+++ b/packages/frontend-app-api/src/wiring/FrontendApiRegistry.ts
@@ -40,6 +40,16 @@ export class FrontendApiRegistry {
     }
   }
 
+  set(factory: AnyApiFactory) {
+    this.factories.set(factory.api.id, factory);
+  }
+
+  setAll(factories: Iterable<AnyApiFactory>) {
+    for (const factory of factories) {
+      this.set(factory);
+    }
+  }
+
   get<T>(
     api: ApiRef<T>,
   ): ApiFactory<T, T, { [name: string]: unknown }> | undefined {
@@ -80,6 +90,17 @@ export class FrontendApiResolver implements ApiHolder {
     return this.load(ref);
   }
 
+  invalidate(apiRefIds?: Iterable<string>) {
+    if (apiRefIds === undefined) {
+      this.apis.clear();
+      return;
+    }
+
+    for (const apiRefId of apiRefIds) {
+      this.apis.delete(apiRefId);
+    }
+  }
+
   private load<T>(ref: ApiRef<T>, loading: AnyApiRef[] = []): T | undefined {
     const existing = this.apis.get(ref.id);
     if (existing) {
diff --git a/packages/frontend-app-api/src/wiring/createErrorCollector.ts b/packages/frontend-app-api/src/wiring/createErrorCollector.ts
index 5f081bc092..1867507948 100644
--- a/packages/frontend-app-api/src/wiring/createErrorCollector.ts
+++ b/packages/frontend-app-api/src/wiring/createErrorCollector.ts
@@ -82,6 +82,12 @@ export type AppErrorTypes = {
       existingPluginId: string;
     };
   };
+  EXTENSION_BOOTSTRAP_PREDICATE_IGNORED: {
+    context: { node: AppNode };
+  };
+  EXTENSION_BOOTSTRAP_API_UNAVAILABLE: {
+    context: { node: AppNode; apiRefId: string };
+  };
   // routing
   ROUTE_DUPLICATE: {
     context: { routeId: string };
diff --git a/packages/frontend-defaults/src/maybeCreateErrorPage.tsx b/packages/frontend-defaults/src/maybeCreateErrorPage.tsx
index 152c37fdd3..8c058b838f 100644
--- a/packages/frontend-defaults/src/maybeCreateErrorPage.tsx
+++ b/packages/frontend-defaults/src/maybeCreateErrorPage.tsx
@@ -24,6 +24,8 @@ const DEFAULT_WARNING_CODES: Array<keyof AppErrorTypes> = [
   'EXTENSION_INPUT_DATA_IGNORED',
   'EXTENSION_INPUT_INTERNAL_IGNORED',
   'EXTENSION_OUTPUT_IGNORED',
+  'EXTENSION_BOOTSTRAP_PREDICATE_IGNORED',
+  'EXTENSION_BOOTSTRAP_API_UNAVAILABLE',
 ];
 
 function AppErrorItem(props: { error: AppError }): JSX.Element {