He then moved to USC, where he was an assistant to Mike Gillespie for four seasons, during which the Trojans appeared in four NCAA tournaments and reached the 1995 College World Series final.

Loyola Marymount named Cruz head coach in 1997, and he led the Lions to three straight first-place finishes in the West Coast Conference from 1998–2000.

In addition to his duties at LMU, Cruz was head coach of USA Baseball's 2004 national team, winning the program's first gold medal at the FISU World University Championships.

Following twelve successful years at LMU, Cruz became a volunteer assistant at USC for the 2009 and 2010 seasons under head coach Chad Kreuter.

[5] He was fired for knowingly exceeding the number of hours of scheduled practices after a weeklong investigation by the USC athletic department.