Click on the ‘Settings’ icon in the top right corner of Auto FTP Manager. On the General settings tab, select ‘On Application close, minimize Auto FTP Manager to system tray’. The application will be minimized to the system tray when you close it. All your transfers and ongoing processes will continue to run in the background. In order to restore the program, click on the application icon in the system tray.

You can also select the ‘On Application launch, minimize Auto FTP Manager to system tray’ option to keep the application running in the background on launch.