Mota attended Cal State Fullerton in Orange County on a baseball scholarship. He was drafted in the second round of the 1985 amateur draft by the Chicago White Sox. He spent time in the Texas Rangers and Los Angeles Dodgers organizations before being drafted by the Oakland Athletics in with the rule 5 draft. He was then sent to the San Diego Padres in in a three-team trade and made his major league debut in with the Padres. He later signed with the Kansas City Royals as a free agent, but only appeared in two games in . Mota's father, Manny, and brother, Andy are also former Major League players, as is his cousin, José Báez.