diff --git a/src/core/packages/chrome/navigation/src/components/popover/index.tsx b/src/core/packages/chrome/navigation/src/components/popover/index.tsx
index bc0d204ca339b..c2d1f752bedbb 100644
--- a/src/core/packages/chrome/navigation/src/components/popover/index.tsx
+++ b/src/core/packages/chrome/navigation/src/components/popover/index.tsx
@@ -191,8 +191,9 @@ export const SideNavPopover = ({
       const isStayingInComponent =
         nextFocused &&
         (triggerRef.current?.contains(nextFocused) || popoverRef.current?.contains(nextFocused));
+      const isTrappedByFlyout = (nextFocused as HTMLElement)?.classList.contains('euiFlyout');
 
-      if (!isStayingInComponent) {
+      if (!isStayingInComponent && !isTrappedByFlyout) {
         handleClose();
       }
     },