In 1991, Esquer was hired by his college coach Mark Marquess as an assistant coach. In 1996, he was hired as an assistant coach of Pepperdine University's baseball team, handling recruiting, hitting instruction, infield coaching, and third base coach duties.
Following the 1999 season, Esquer was hired as head baseball coach at Cal. Through the 2010 season, Esquer has a career record of 316-290-2 (.521), has led the Bears to NCAA Regionals in 2001, 2008, and 2010, and was named Pacific-10 Conference coach of the year in 2001. In 2011, Esquer led the Bears back to their first College World Series appearance since 1992 and was named national baseball coach of the year by the National College Baseball Writers Association.
National champion Postseason invitational champion Conference regular season champion Conference regular season and conference tournament champion Division regular season champion Division regular season and conference tournament champion Conference tournament champion