Short answer: in almost every case the app is still running and its icon has nowhere to be drawn. The usual causes are the MacBook notch eating the overflow, a menu bar manager hiding it, the app's own "show icon" setting being off, or the app having quit. Work through the checks below in order — they are sorted by how often each turns out to be the culprit.
Check 1: is the menu bar simply full?
Switch to Finder and look again.
Finder has one of the shortest menu bars in macOS. If the missing icon reappears, nothing is wrong with the app — you have more status items than fit alongside the previous app's menus. On a notched MacBook this is by far the most common cause, and macOS never says a word about it.
Read why the notch hides menu bar icons for the six ways to get that space back, or install a manager that counts and names the missing items so you stop guessing.
Check 2: is a menu bar manager hiding it?
If you run Pelmet, Ice, Hidden Bar, Bartender, or Vanilla, the icon may be collapsed behind its divider.
- Pelmet — press ⌥⌘B or click the
‹chevron. If the icon appears, it was simply on the hidden side of the╱. Command-drag it to the right of the divider to keep it visible. - Others — click the manager's own chevron or press its shortcut.
Two managers running at once is its own bug: they fight over the same status items and positions. Quit all but one.
Check 3: is the app actually running?
Open Activity Monitor and search for the app's name, or press ⌘Space and launch it again.
Menu-bar-only apps have no Dock icon and no window, so a crash is completely silent — the icon disappearing is the only symptom. If the app is not in Activity Monitor, it is not running. Launch it and see whether the icon returns.
Check 4: has the app been told not to show an icon?
Most menu bar apps have a preference like "Show icon in menu bar", and some ship with it off, or turn it off during an update.
Open the app's settings and look for it. Many apps let you reopen settings by launching the app again while it is already running.
Check 5: was the icon Command-dragged off the bar?
Holding Command and dragging an icon out of the menu bar removes it. This is easy to do by accident while rearranging.
The fix depends on the app: some restore the icon when relaunched, others have a setting to bring it back. If neither works, quit and relaunch the app.
Check 6: is it an Apple icon you removed from Control Center?
Wi-Fi, Bluetooth, Sound, Battery, Focus, Screen Mirroring, the clock, Spotlight, Siri and Time Machine are all governed by System Settings → Control Center. If one of those is missing, set it to Show in Menu Bar there.
Check 7: is the app a login item that stopped starting?
If the icon is missing after every restart rather than mid-session, the app is probably no longer launching at login.
Open System Settings → General → Login Items & Extensions and confirm it is listed and enabled. macOS occasionally disables login items after an app update changes its signature.
Check 8: restart the menu bar process
Rare, but real: the process that draws menu bar extras can get into a bad state. Restarting it is harmless — the bar redraws in a second.
killall SystemUIServer
Only Apple's own menu bar extras are managed by that process, so this will not affect third-party icons. If a third-party icon is stuck, quit and relaunch that app instead.
Still missing?
If you have worked through all eight and an icon is still gone, it is almost certainly the notch — the case with no built-in indicator at all.
Pelmet is the only menu bar tool that reports it: a +N badge next to its chevron when items do not fit, and the Shelf, which names every one by its application. It is free, MIT licensed, and needs no permissions to do it.