I set antimicrox and qbittorrent to autostart and they have start in tray on but on login they start in windows and quit on close not close to tray
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This is a bug in Waybar, which I suppose you are using. When app create tray icon before Waybar finish launching it is not shown.
Create a script like autostart.sh, start waybar there, then do like 5 second delay and start apps that has tray icons.