Following his playing career, Gonzales joined the coaching staff at the New Mexico as a
graduate assistant from 1999 to 2002. He served as the team's video coordinator from 2003 to 2005. He was then promoted to a full-time assistant, coaching the team's
safeties,
kickers,
punters and
long snappers from 2006 to 2008. In 2011, Gonzales joined
Rocky Long's staff at
San Diego State University. He coached the
safeties for six seasons, before being promoted to
defensive coordinator prior to the 2017 season. He continued to coach the safeties. In 2018, Gonzales was hired as a part of
Herm Edwards' first staff at
Arizona State University to serve as the
defensive coordinator. On December 17, 2019, Gonzales was hired as the Lobo's new head coach, replacing
Bob Davie. On November 25, 2023, Gonzales was relieved from his position at the University of New Mexico after serving as head coach for four years. On January 25, 2024, Gonzales was hired to join
Brent Brennan and the
University of Arizona as the special teams coordinator and
linebackers coach. ==Head coaching record==