diff --git a/core/src/components.d.ts b/core/src/components.d.ts
index d1e2462378a..d1dca6a73a8 100644
--- a/core/src/components.d.ts
+++ b/core/src/components.d.ts
@@ -334,6 +334,7 @@ export namespace Components {
         "mode"?: "ios" | "md";
         /**
           * Used to set focus on an element that uses `ion-focusable`. Do not use this if focusing the element as a result of a keyboard event as the focus utility should handle this for us. This method should be used when we want to programmatically focus an element as a result of another user action. (Ex: We focus the first element inside of a popover when the user presents it, but the popover is not always presented as a result of keyboard action.)
+          * @param elements - The elements to set focus on.
          */
         "setFocus": (elements: HTMLElement[]) => Promise<void>;
         /**
diff --git a/core/src/components/app/app.tsx b/core/src/components/app/app.tsx
index 756f010bdca..c4aabed0722 100644
--- a/core/src/components/app/app.tsx
+++ b/core/src/components/app/app.tsx
@@ -1,6 +1,6 @@
 import type { ComponentInterface } from '@stencil/core';
 import { Component, Element, Host, Method, h } from '@stencil/core';
-import { getOrInitFocusVisibleUtility } from '@utils/focus-visible';
+import { focusElements } from '@utils/focus-visible';
 
 import { config } from '../../global/config';
 import { getIonTheme } from '../../global/ionic-global';
@@ -24,11 +24,16 @@ export class App implements ComponentInterface {
    * a result of another user action. (Ex: We focus the first element
    * inside of a popover when the user presents it, but the popover is not always
    * presented as a result of keyboard action.)
+   *
+   * @param elements - The elements to set focus on.
    */
   @Method()
   async setFocus(elements: HTMLElement[]) {
-    const focusVisible = getOrInitFocusVisibleUtility();
-    focusVisible.setFocus(elements);
+    /**
+     * The focus-visible utility is used to set focus on an
+     * element that uses `ion-focusable`.
+     */
+    focusElements(elements);
   }
 
   render() {
diff --git a/core/src/utils/focus-visible.ts b/core/src/utils/focus-visible.ts
index 259518789cb..3fba715defe 100644
--- a/core/src/utils/focus-visible.ts
+++ b/core/src/utils/focus-visible.ts
@@ -30,6 +30,22 @@ export const getOrInitFocusVisibleUtility = () => {
   return focusVisibleUtility;
 };
 
+/**
+ * Used to set focus on an element that uses `ion-focusable`.
+ * Do not use this if focusing the element as a result of a keyboard
+ * event as the focus utility should handle this for us. This method
+ * should be used when we want to programmatically focus an element as
+ * a result of another user action. (Ex: We focus the first element
+ * inside of a popover when the user presents it, but the popover is not always
+ * presented as a result of keyboard action.)
+ *
+ * @param elements - The elements to set focus on.
+ */
+export const focusElements = (elements: Element[]) => {
+  const focusVisible = getOrInitFocusVisibleUtility();
+  focusVisible.setFocus(elements);
+};
+
 export const startFocusVisible = (rootEl?: HTMLElement): FocusVisibleUtility => {
   let currentFocus: Element[] = [];
   let keyboardMode = true;
diff --git a/core/src/utils/helpers.ts b/core/src/utils/helpers.ts
index c57c95a70c5..292895c99d5 100644
--- a/core/src/utils/helpers.ts
+++ b/core/src/utils/helpers.ts
@@ -1,4 +1,5 @@
 import type { EventEmitter } from '@stencil/core';
+import { focusElements } from '@utils/focus-visible';
 
 import type { Side } from '../components/menu/menu-interface';
 import { config } from '../global/config';
@@ -255,6 +256,17 @@ export const hasShadowDom = (el: HTMLElement) => {
   return !!el.shadowRoot && !!(el as any).attachShadow;
 };
 
+/**
+ * Focuses a given element while ensuring proper focus management
+ * within the Ionic framework. If the element is marked as `ion-focusable`,
+ * this function will delegate focus handling to `ion-app` or manually
+ * apply focus when a custom app root is used.
+ *
+ * This function helps maintain accessibility and expected focus behavior
+ * in both standard and custom root environments.
+ *
+ * @param el - The element to focus.
+ */
 export const focusVisibleElement = (el: HTMLElement) => {
   el.focus();
 
@@ -267,10 +279,35 @@ export const focusVisibleElement = (el: HTMLElement) => {
    * which will let us explicitly set the elements to focus.
    */
   if (el.classList.contains('ion-focusable')) {
-    const appRootSelector = config.get('appRootSelector', 'ion-app');
+    const appRootSelector: string = config.get('appRootSelector', 'ion-app');
     const app = el.closest(appRootSelector) as HTMLIonAppElement | null;
     if (app) {
-      app.setFocus([el]);
+      if (appRootSelector === 'ion-app') {
+        /**
+         * If the app root is the default, then it will be
+         * in charge of setting focus. This is because the
+         * focus-visible utility is attached to the app root
+         * and will handle setting focus on the correct element.
+         */
+        app.setFocus([el]);
+      } else {
+        /**
+         * When using a custom app root selector, the focus-visible
+         * utility is not available to manage focus automatically.
+         * If we set focus immediately, the element may not be fully
+         * rendered or interactive, especially if it was just added
+         * to the DOM. Using requestAnimationFrame ensures that focus
+         * is applied on the next frame, allowing the DOM to settle
+         * before changing focus.
+         */
+        requestAnimationFrame(() => {
+          /**
+           * The focus-visible utility is used to set focus on an
+           * element that uses `ion-focusable`.
+           */
+          focusElements([el]);
+        });
+      }
     }
   }
 };