Magee began his coaching career after being discharged by serving the role of the Director of Player Personnel at his alma mater until 2016. In 2017 he first arrived in Ann Arbor as the Associate Athletic Director for Football where he assisted with roster construction and providing oversight and direction for off-field activities. In May 2022 he was hired by the Chicago Bears as chief of staff to Matt Eberflus. During his tenure in Chicago, the Bears went 10-24. The following year Magee left Chicago to take the position of general manager for the Michigan Wolverines. In November 2024 he was instrumental in the transfer of quarterback Bryce Underwood from LSU.