A system and methods are described for transcoding media content in the background on a source computer device prior to such time as a target media playback device is connected to the source computer for synchronization of the media content. The system and methods anticipate which media content to background-transcode based on user input rules and media status data that are maintained in a transcode database. Pre-transcoding media content provides advantages that include a significant reduction in the time needed to synchronize media content between a source computer and a target media playback device, and an efficient use of CPU power for transcoding media content at times when the CPU might otherwise stand idle.