Mota was originally signed by the New York Mets in 1990 as an infielder. After several years in their organization, he was drafted by the Montreal Expos in the Rule 5 draft in 1996 and converted into a pitcher in 1997. Mota had a 2.96 ERA in 1999, his rookie season, but he struggled in his next two seasons and was traded to the Los Angeles Dodgers prior to 2002. His struggles continued in his first year with the Dodgers, but Mota had a career year in 2003, as he had a 6–3 record with a 1.97 ERA in 76 games. He became the setup man to closer Éric Gagné in 2004, but was traded to the Florida Marlins midseason. Mota started 2005 as their closer, but Todd Jones took over the role when Mota got hurt in April. Following the year, Mota was traded to the Boston Red Sox.