[3] In 2014, he became an assistant for the United States senior team under Jürgen Klinsmann[4][5][6] In December 2015, he was named assistant coach of New York City FC of Major League Soccer under Patrick Vieira,[7][8] remaining with the club after Vieria's departure under Domènec Torrent .
[9] In 2021, he joined Toronto FC as an assistant under new coach Chris Armas.
[10][11] On 7 July, in his debut as head coach, Toronto defeated the New England Revolution by a score of 3–2.
[12][13] On 9 August, he was officially named the head coach for the remainder of the season, removing the interim title.
[20] Pérez wrote the U.S. Soccer Coaching Curriculum with Claudio Reyna.