diff --git a/platform/linuxbsd/x11/display_server_x11.cpp b/platform/linuxbsd/x11/display_server_x11.cpp
index 34b6d0219a5..4d7ee97e78b 100644
--- a/platform/linuxbsd/x11/display_server_x11.cpp
+++ b/platform/linuxbsd/x11/display_server_x11.cpp
@@ -4190,8 +4190,11 @@ void DisplayServerX11::popup_open(WindowID p_window) {
 		}
 	}
 
+	// Detect tooltips and other similar popups that shouldn't block input to their parent.
+	bool ignores_input = window_get_flag(WINDOW_FLAG_NO_FOCUS, p_window) && window_get_flag(WINDOW_FLAG_MOUSE_PASSTHROUGH, p_window);
+
 	WindowData &wd = windows[p_window];
-	if (wd.is_popup || has_popup_ancestor) {
+	if (wd.is_popup || (has_popup_ancestor && !ignores_input)) {
 		// Find current popup parent, or root popup if new window is not transient.
 		List<WindowID>::Element *C = nullptr;
 		List<WindowID>::Element *E = popup_list.back();
diff --git a/platform/macos/display_server_macos.mm b/platform/macos/display_server_macos.mm
index 50313cfe67a..3c394fe183b 100644
--- a/platform/macos/display_server_macos.mm
+++ b/platform/macos/display_server_macos.mm
@@ -3430,8 +3430,11 @@ void DisplayServerMacOS::popup_open(WindowID p_window) {
 		}
 	}
 
+	// Detect tooltips and other similar popups that shouldn't block input to their parent.
+	bool ignores_input = window_get_flag(WINDOW_FLAG_NO_FOCUS, p_window) && window_get_flag(WINDOW_FLAG_MOUSE_PASSTHROUGH, p_window);
+
 	WindowData &wd = windows[p_window];
-	if (wd.is_popup || has_popup_ancestor) {
+	if (wd.is_popup || (has_popup_ancestor && !ignores_input)) {
 		bool was_empty = popup_list.is_empty();
 		// Find current popup parent, or root popup if new window is not transient.
 		List<WindowID>::Element *C = nullptr;
diff --git a/platform/windows/display_server_windows.cpp b/platform/windows/display_server_windows.cpp
index 4a482f560c2..12182fc80ab 100644
--- a/platform/windows/display_server_windows.cpp
+++ b/platform/windows/display_server_windows.cpp
@@ -3574,8 +3574,11 @@ void DisplayServerWindows::popup_open(WindowID p_window) {
 		}
 	}
 
+	// Detect tooltips and other similar popups that shouldn't block input to their parent.
+	bool ignores_input = window_get_flag(WINDOW_FLAG_NO_FOCUS, p_window) && window_get_flag(WINDOW_FLAG_MOUSE_PASSTHROUGH, p_window);
+
 	WindowData &wd = windows[p_window];
-	if (wd.is_popup || has_popup_ancestor) {
+	if (wd.is_popup || (has_popup_ancestor && !ignores_input)) {
 		// Find current popup parent, or root popup if new window is not transient.
 		List<WindowID>::Element *C = nullptr;
 		List<WindowID>::Element *E = popup_list.back();