The disclosure provides for transitioning application windows between local and remote desktops. Example implementations include opening a first file with a first application to generate a first application window on a first desktop window on a user display; based at least on a trigger event for transitioning the first application window from the first desktop window to a second desktop window, determining whether a second application is available for the second desktop window to produce a version of the first application window; and based at least on the second application being available: transferring the first file across a network to become a second file; and opening the second file with the second application to generate a second application window on the second desktop window, the second application window replacing the first application window on the user display. The transition may go either direction.