diff --git a/cypress/e2e/theming/admin-settings_background.cy.ts b/cypress/e2e/theming/admin-settings_background.cy.ts
index e4ec661486f..52c27aaed8a 100644
--- a/cypress/e2e/theming/admin-settings_background.cy.ts
+++ b/cypress/e2e/theming/admin-settings_background.cy.ts
@@ -175,9 +175,15 @@ describe('Remove the default background with a bright color', function() {
 	})
 
 	it('See the header being inverted', function() {
+		// Probe the Nextcloud logo: it carries the same
+		// `var(--background-image-invert-if-bright)` filter and is always
+		// present in the header. The waffle launcher's current-app icon only
+		// renders when an app is active, which isn't the case on settings,
+		// and the in-popover tiles use a fixed brightness/invert filter
+		// regardless of theme so they're not a valid inversion probe.
 		cy.waitUntil(() => navigationHeader
-			.getNavigationEntries()
-			.find('img')
+			.logo()
+			.find('.logo')
 			.then((el) => {
 				let ret = true
 				el.each(function() {
diff --git a/cypress/e2e/theming/user-settings_app-order.cy.ts b/cypress/e2e/theming/user-settings_app-order.cy.ts
index 3db1a17ac4e..5098b9af431 100644
--- a/cypress/e2e/theming/user-settings_app-order.cy.ts
+++ b/cypress/e2e/theming/user-settings_app-order.cy.ts
@@ -35,9 +35,14 @@ describe('User theming set app order', () => {
 		const appOrder = ['Dashboard', 'Files']
 		appOrderList.assertAppOrder(appOrder)
 
-		// Check the top app menu order
-		navigationHeader.getNavigationEntries()
-			.each((entry, index) => expect(entry).contain.text(appOrder[index]!))
+		// Check the top app menu order. The launcher grid appends a synthetic
+		// "More apps" / "App store" tile to the user's apps, so iterate
+		// positionally only over the real-app prefix.
+		navigationHeader.getNavigationEntries().then(($entries) => {
+			appOrder.forEach((name, index) => {
+				expect($entries.eq(index)).to.contain.text(name)
+			})
+		})
 	})
 
 	it('Change the app order', () => {
@@ -59,9 +64,14 @@ describe('User theming set app order', () => {
 			.scrollIntoView()
 		appOrderList.assertAppOrder(appOrder)
 
-		// Check the top app menu order
-		navigationHeader.getNavigationEntries()
-			.each((entry, index) => expect(entry).contain.text(appOrder[index]!))
+		// Check the top app menu order. Idempotent open in the page object
+		// re-opens the popover after the reload above. The synthetic trailing
+		// tile is ignored by iterating only over the expected app names.
+		navigationHeader.getNavigationEntries().then(($entries) => {
+			appOrder.forEach((name, index) => {
+				expect($entries.eq(index)).to.contain.text(name)
+			})
+		})
 	})
 })
 
@@ -140,9 +150,13 @@ describe('User theming set app order with default app', () => {
 		cy.reload()
 
 		const appOrder = ['Files', 'Test App', 'Dashboard', 'Test App 2']
-		// Check the top app menu order
-		navigationHeader.getNavigationEntries()
-			.each((entry, index) => expect(entry).contain.text(appOrder[index]!))
+		// Check the top app menu order. See note above: the launcher appends
+		// a synthetic tile that we skip by iterating positionally.
+		navigationHeader.getNavigationEntries().then(($entries) => {
+			appOrder.forEach((name, index) => {
+				expect($entries.eq(index)).to.contain.text(name)
+			})
+		})
 	})
 })
 
@@ -219,9 +233,12 @@ describe('User theming reset app order', () => {
 		const appOrder = ['Dashboard', 'Files']
 		appOrderList.assertAppOrder(appOrder)
 
-		// Check the top app menu order
-		navigationHeader.getNavigationEntries()
-			.each((entry, index) => expect(entry).contain.text(appOrder[index]!))
+		// Check the top app menu order. See note above on the synthetic tile.
+		navigationHeader.getNavigationEntries().then(($entries) => {
+			appOrder.forEach((name, index) => {
+				expect($entries.eq(index)).to.contain.text(name)
+			})
+		})
 	})
 
 	it('See the reset button is disabled', () => {
@@ -263,9 +280,12 @@ describe('User theming reset app order', () => {
 	it('See the app order is restored', () => {
 		const appOrder = ['Dashboard', 'Files']
 		appOrderList.assertAppOrder(appOrder)
-		// Check the top app menu order
-		navigationHeader.getNavigationEntries()
-			.each((entry, index) => expect(entry).contain.text(appOrder[index]!))
+		// Check the top app menu order. See note above on the synthetic tile.
+		navigationHeader.getNavigationEntries().then(($entries) => {
+			appOrder.forEach((name, index) => {
+				expect($entries.eq(index)).to.contain.text(name)
+			})
+		})
 	})
 
 	it('See the reset button is disabled again', () => {
diff --git a/cypress/e2e/theming/user-settings_background.cy.ts b/cypress/e2e/theming/user-settings_background.cy.ts
index 639de55f571..2ad00230472 100644
--- a/cypress/e2e/theming/user-settings_background.cy.ts
+++ b/cypress/e2e/theming/user-settings_background.cy.ts
@@ -131,7 +131,13 @@ describe('User select a bright custom color and remove background', function() {
 	})
 
 	it('See the header being inverted', function() {
-		cy.waitUntil(() => navigationHeader.getNavigationEntries().find('img').then((el) => {
+		// Probe the Nextcloud logo: it carries the same
+		// `var(--background-image-invert-if-bright)` filter and is always
+		// present in the header. The waffle launcher's current-app icon only
+		// renders when an app is active, which isn't the case on settings,
+		// and the in-popover tiles use a fixed brightness/invert filter
+		// regardless of theme so they're not a valid inversion probe.
+		cy.waitUntil(() => navigationHeader.logo().find('.logo').then((el) => {
 			let ret = true
 			el.each(function() {
 				ret = ret && window.getComputedStyle(this).filter === 'invert(1)'
@@ -157,7 +163,9 @@ describe('User select a bright custom color and remove background', function() {
 	})
 
 	it('See the header NOT being inverted this time', function() {
-		cy.waitUntil(() => navigationHeader.getNavigationEntries().find('img').then((el) => {
+		// Probe the Nextcloud logo: see the inverted-header test above for
+		// why we don't probe the menu icons.
+		cy.waitUntil(() => navigationHeader.logo().find('.logo').then((el) => {
 			let ret = true
 			el.each(function() {
 				ret = ret && window.getComputedStyle(this).filter === 'none'
diff --git a/cypress/pages/NavigationHeader.ts b/cypress/pages/NavigationHeader.ts
index 330dc58eefc..e911a597ce4 100644
--- a/cypress/pages/NavigationHeader.ts
+++ b/cypress/pages/NavigationHeader.ts
@@ -4,7 +4,11 @@
  */
 
 /**
- * Page object model for the Nextcloud navigation header
+ * Page object model for the Nextcloud navigation header.
+ *
+ * The app launcher (waffle menu) is an NcPopover whose content is teleported
+ * to <body>, so the menu items do not live inside the <nav> element. Selectors
+ * for the menu entries scope to the popover rather than the nav.
  */
 export class NavigationHeader {
 	/**
@@ -23,35 +27,91 @@ export class NavigationHeader {
 	}
 
 	/**
-	 * Locator of the app navigation bar
+	 * Locator of the app navigation bar.
+	 *
+	 * The accessible name is just "Applications" since the waffle redesign;
+	 * the previous label "Applications menu" is gone.
 	 */
 	navigation() {
 		return this.header()
-			.findByRole('navigation', { name: 'Applications menu' })
+			.findByRole('navigation', { name: 'Applications' })
 	}
 
 	/**
-	 * The toggle for the navigation overflow menu
+	 * Open the waffle launcher popover.
+	 *
+	 * Idempotent: if the popover is already open the click is skipped, so
+	 * callers can invoke this defensively at the start of any helper that
+	 * needs the menu items in the DOM.
+	 */
+	openMenu() {
+		this.navigation()
+			.find('.app-menu__waffle')
+			.then(($trigger) => {
+				if ($trigger.attr('aria-expanded') !== 'true') {
+					cy.wrap($trigger).click()
+				}
+			})
+		// Popover is teleported to <body>, so query from the document root.
+		cy.get('.app-menu__popover').should('be.visible')
+		return this.popover()
+	}
+
+	/**
+	 * Close the waffle launcher popover.
+	 *
+	 * Sends Escape rather than clicking outside: NcPopover's focus trap is
+	 * active while the menu is open, so a stray click can land on a tile.
+	 */
+	closeMenu() {
+		cy.get('body').type('{esc}')
+		cy.get('.app-menu__popover').should('not.exist')
+	}
+
+	/**
+	 * Locator for the popover content (the teleported grid wrapper).
+	 *
+	 * Scoping menu-item queries here is mandatory: the popover is rendered
+	 * outside the <nav>, so `.within(navigation())` would find nothing.
+	 */
+	popover() {
+		return cy.get('[role="menu"][aria-label="Apps"]')
+	}
+
+	/**
+	 * The waffle trigger that toggles the launcher.
+	 *
+	 * @deprecated The old "overflow" affordance is gone; this now points at
+	 *   the waffle button so existing call sites keep compiling. Prefer
+	 *   {@link openMenu} / {@link closeMenu} in new code.
 	 */
 	overflowNavigationToggle() {
 		return this.navigation()
+			.find('.app-menu__waffle')
 	}
 
 	/**
-	 * Get all navigation entries
+	 * Get all navigation entries in the launcher.
+	 *
+	 * Opens the popover first if it is not already open; the entries do not
+	 * exist in the DOM otherwise. Each entry is rendered as an `<a role="menuitem">`.
 	 */
 	getNavigationEntries() {
-		return this.navigation()
-			.findAllByRole('listitem')
+		this.openMenu()
+		return this.popover().findAllByRole('menuitem')
 	}
 
 	/**
-	 * Get the navigation entry for a given app
+	 * Get the navigation entry for a given app.
+	 *
+	 * Each tile's accessible name comes from the `<a title="...">` attribute
+	 * and the inner `.app-item__label`, so `findByRole('menuitem', { name })`
+	 * matches reliably.
 	 *
 	 * @param name The app name
 	 */
 	getNavigationEntry(name: string) {
-		return this.navigation()
-			.findByRole('listitem', { name })
+		this.openMenu()
+		return this.popover().findByRole('menuitem', { name })
 	}
 }