In 1986, Larrañaga left Virginia for the head coaching job at Bowling Green State University. In his first season there, the Falcons improved by eight games over the 1985–86 season, finishing 15–14. He went on to record a 170–144 record in 11 years there, and was only the second coach in Bowling Green history to take the Falcons to postseason play in consecutive years (the 1990 and 1991 editions of the NIT). During his tenure at Bowling Green the Falcons defeated the perennial national powers Kentucky, Michigan State (twice), Ohio State, Penn State and Purdue. In his final season at Bowling Green (1996–97), he led the Falcons to a regular-season co-championship in the Mid-American Conference and another NIT berth, and was also named the conference's Coach of the Year. He is still the second-winningest coach in school history (behind only Hall of Famer Harold Anderson), as well as one of the winningest coaches in the Mid-American Conference. One notable NBA player who played for Larrañaga was guard Antonio Daniels, who was selected fourth overall in the 1997 draft.