After retiring, Cabrera settled permanently in the United States to pursue work as a helicopter pilot in the New York area. He began working with the Major League Soccer front office as a community development manager working on Hispanic grassroots and youth programs. He also worked as an assistant coach for the Suffolk County Community College men's soccer team as well as top-ranked youth soccer club B.W. Gottschee, based in Queens, New York.[5]
Cabrera earned his United States Soccer Federation A Coaching License in 2005 and became an assistant coach with the United States men's national under-18 soccer team in 2007.[1] He was named by the USSF as head coach of the United States men's national under-17 soccer team on October 25, 2007, becoming the first Latin American head coach in the U.S. national team system.[4] On January 24, 2012, he was replaced in this role by Richie Williams.[5]
In January 2012, Cabrera was named assistant coach for the Colorado Rapids of Major League Soccer.[6]
In January 2014, Chivas USA appointed Cabrera as head coach.[7] The club was dissolved by the league at the end of the season, with Cabrera's team finishing seventh in the Western Conference, the highest finish for Chivas USA in their final five seasons.[8]
Cabrera was named head coach of the Rio Grande Valley FC Toros of the United Soccer League on December 2, 2015.[9]
Cabrera was named head coach of the Houston Dynamo on October 28, 2016.[10] He and the Dynamo parted ways on August 13, 2019.[11]
Cabrera became head coach of the Montreal Impact on August 21, 2019.[12] On October 24, 2019, the Impact announced that his contract would not be renewed for the 2020 season.[13]