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 b2ca81f63e7a3..265f39aa88bbb 100644
--- a/src/core/packages/chrome/navigation/src/components/popover/index.tsx
+++ b/src/core/packages/chrome/navigation/src/components/popover/index.tsx
@@ -194,8 +194,15 @@ export const SideNavPopover = ({
           triggerRef.current?.contains(nextFocused) || popoverRef.current?.contains(nextFocused)
         );
       const isTrappedByFlyout = (nextFocused as HTMLElement)?.classList.contains('euiFlyout');
-
-      if (isStayingInComponent === false && isTrappedByFlyout === false) {
+      const isTrappedByPageOverlay = !!(nextFocused as HTMLElement)?.closest(
+        '.securitySolution-pageOverlay'
+      );
+
+      if (
+        isStayingInComponent === false &&
+        isTrappedByFlyout === false &&
+        isTrappedByPageOverlay === false
+      ) {
         handleClose();
       }
     },