In 1990, Garcia transferred to San Jose State University and redshirted his first year there. From 1991 to 1993, Garcia was starting quarterback on the San Jose State Spartans football team. Under Garcia, San Jose State went 6-4-1 in 1991, 7–4 in 1992, and 2–9 in 1993. In 1991, Garcia had a career-high 61.9% completion rate at San Jose State with 99-for-160 passing for 1,519 yards, 12 touchdowns, and 5 interceptions. He passed for 2,418 yards in 1992 on 209-for-371 passing with 15 touchdowns and 11 interceptions and a career-high 2,608 yards in 1993 on 196-for-356 passing, 21 touchdowns, and 16 interceptions. For his junior season in 1992, Garcia earned UPI All-America honors. As of 2007, Garcia had the most career offensive yards (7,274) in San Jose State history.