When two windows are both set to always on top, Windows does not pick a permanent winner. Both sit above every normal window, and between the two of them, the one you clicked or activated most recently goes in front. There is no “more on top” setting, so the practical fix is to decide which window you pin and lay them out so they do not overlap, which is what PinPoint from Automata Labs is built to manage with per-app rules, colored borders and profiles.
Pin the windows you need, see at a glance which ones are pinned, and stop them fighting for the top spot.
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How does Windows decide which window is on top?
Every top-level window on your desktop has a position in a stack Microsoft calls the z-order. In its Window Features documentation, Microsoft describes it as “a stack of overlapping windows” along an imaginary axis coming out of the screen. The window at the top of the z-order overlaps all the others.
The same page explains that the system keeps that stack in a single list and sorts windows into groups. The group that matters here is topmost windows, which is what an always on top window is:
“A topmost window overlaps all other non-topmost windows, regardless of whether it is the active or foreground window.”
Microsoft adds that “all topmost windows appear in the z-order before any non-topmost windows.” In plain terms, there are two layers on your desktop: a top layer for pinned windows and a normal layer for everything else. Nothing in the normal layer can cover anything in the top layer.
What happens when two pinned windows overlap?
Inside the top layer, the ordinary rules apply again. Microsoft’s documentation says “the system positions the active window at the top of the z-order for windows of the same type,” and that when an application creates a window, the system puts it at the top of the z-order for windows of the same type.
So with two pinned windows, for example a video call and a sticky note:
- Both float above your browser, editor and every other normal window.
- When you click the sticky note, it moves to the top of the pinned layer and covers the call where they overlap.
- When you click the call, the order flips back.
- A newly opened pinned window starts at the top of the pinned layer.
Neither window is broken, and neither app is ignoring your pin. They are simply taking turns at the top of the same layer, in the order you use them.
Can I make one window stay above all other always on top windows?
Not with a standard setting. Microsoft engineer Raymond Chen has written about this exact request on The Old New Thing. In What if two programs did this? he walks through the thought experiment: if Program A and Program B both made a “super-topmost” window and you dragged them over each other, “one of those two windows must be above the other,” which contradicts the idea.
In a follow-up, How do I create a topmost window that is never covered by other topmost windows?, he describes a developer whose app kept reasserting itself as topmost and ended up “fighting back and forth” with another app doing the same thing. His conclusion is direct: “There is no ‘super topmost’ flag.”
That matters for you as a user. Any tool that promises its window will always beat every other pinned window is either fighting other apps in a loop, which can cause flicker and focus stealing, or it is not telling the whole story. The reliable approach is to control which windows are pinned and where they sit.
Which windows are often already on top without you knowing?
A surprising number of apps set themselves to topmost, at least some of the time. When a window you pinned keeps getting covered, the cause is usually one of these:
| Window type | Why it may be topmost | What to try |
|---|---|---|
| Video players with a “stay on top” or picture in picture mode | The player sets it in its own settings | Turn the player’s own option off if you are pinning it with another tool, so only one thing controls it |
| Meeting app mini windows and screen share toolbars | Designed to float over your work during calls | Move them to a corner or another monitor rather than fighting them |
| Notifications, toasts and system overlays | Windows shows these above apps | Let them appear and close; they are short lived |
| Screenshot, recording and color picker tools | Overlays need to sit above everything to capture it | Close the tool when you are done |
| Another pinning utility | Two pinning tools controlling the same window | Use one pinning tool at a time |
If you are not sure whether a window is pinned at all, our guide to a window stuck always on top covers how to find out which app pinned it and how to unpin it.
How do I keep the right window visible when several are pinned?
Since the top layer behaves like a normal stack, the fixes are mostly about layout and discipline:
- Pin fewer windows. Pin only the window that must stay visible while you work in something else, such as a call, a reference document or a timer. Every extra pinned window is another one that can cover it.
- Stop pinned windows from overlapping. Put a small pinned window in a corner, or on a second monitor, so the question of which is in front never comes up.
- Size them for their job. A pinned window that is half the screen will cover other pinned windows constantly. Make reference windows narrow and call windows small.
- Click the one you want in front. Because the most recently activated pinned window goes to the top of the pinned layer, a single click is the quickest way to bring the right one forward.
- Use one pinning method per window. If an app has its own always on top option, either use that or a pinning tool, not both, so you know what to switch off later.
The built-in Windows options for pinning are covered in our always on top shortcut guide, and if a shortcut does nothing at all, see always on top not working in Windows 11.
How does PinPoint help with multiple pinned windows?
PinPoint is a Windows app for pinning windows on top with rules, so you set up your layout once instead of repinning by hand. Its Microsoft Store listing describes these features, which map directly onto the problems above:
- Multi-window support. Pin as many windows as you need at the same time, using a customizable global hotkey.
- Custom visual borders. Pinned windows get color-coded borders with adjustable thickness, so you can see at a glance which windows are in the top layer and which are not. That alone answers most “why is this covering that” questions.
- Intelligent auto-pinning. Pick an app from your running process list and PinPoint pins it when it launches, so your call window or reference tool comes up pinned without a keystroke.
- Workspace Pin Profiles. Save curated window layouts for different contexts and switch between them with a click, so the windows pinned during research are not the ones pinned during a call.
- Application exclusion rules. Exclude apps you never want pinned, so secondary panels do not crowd your top layer.
- Timed countdown release. Set a window to unpin itself after a set time, so a temporary pin does not linger and cover things later.
- Audio feedback when you pin and unpin, and a footprint the listing puts at under 14 MB on disk, running fully offline with no account.
Give each pinned window a colored border and a rule, and keep your top layer tidy.
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PinPoint does not claim to break the rules described above, and that is a good thing. It works with Windows’ topmost layer rather than trying to win a fight inside it, which is why borders, profiles and exclusions matter more than any “always first” promise.
What is a good layout for two pinned windows?
A layout that works for most people on one monitor:
| Pinned window | Suggested size | Suggested position |
|---|---|---|
| Video call or webinar | Small, about a quarter of the screen width | Top right corner |
| Timer, checklist or note | Narrow strip | Bottom right corner, below the call |
| Reference document | Narrow column | Left edge, if you need it at all |
The rule of thumb is that pinned windows should share the edges of the screen and leave the middle for the app you are working in. On two monitors, keep pinned windows on the secondary screen and your main work on the primary one. If windows keep opening on the wrong screen in the first place, our guide to apps opening on the wrong monitor explains why.
Frequently asked questions
Why does my pinned window go behind another pinned window?
Because both are in the topmost layer, and within that layer the most recently activated window goes in front. Click the window you want on top, or rearrange them so they do not overlap.
Is there a way to make a window “more always on top” than another?
Not through a supported setting. Microsoft’s Raymond Chen explains that if two programs could both claim a “super-topmost” spot, one would still have to be above the other, and he states there is no “super topmost” flag.
Can a normal window ever cover an always on top window?
Not by normal stacking. Microsoft’s documentation says a topmost window overlaps all non-topmost windows, even when it is not the active window. If a normal-looking window covers your pinned one, that window is probably topmost too.
Does PinPoint stop other apps from setting themselves on top?
The listing does not claim that. PinPoint pins the windows you choose, shows them with borders, and lets you exclude apps from pinning. Apps that set their own topmost style still do so.
How many windows can I pin with PinPoint?
The Store listing says PinPoint supports pinning as many windows as you need at the same time.
Try PinPoint
Get PinPoint from the Microsoft Store. It is a one-time purchase with no subscription, and the Store listing shows the current price.
Pin windows with rules, borders and timers, and keep the right one in view.
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Microsoft and Windows are trademarks of the Microsoft group of companies. PinPoint is not affiliated with or endorsed by Microsoft.
Last updated 24 October 2026. Published by Automata Labs, a software company in Canada.