José Miguel, who has boxed for most of his career under the shadow of his brother, trains at Bairoa Gym in Caguas. In 1995, he participated at the Pan American Games in Mar Del Plata, Argentina.
On July 25, 2003, José Miguel was supposed to fight in Phoenix, Arizona. However, his opponent had trouble getting a license to fight, as he had been knocked out recently and was serving a 45 day suspension from another state. The Arizona boxing commission was not able to find Cotto an opponent in time and the fight got cancelled.
On September 5, at his native Caguas, Cotto finally returned to action, with a first round knockout win over Johnny Walker.
On December 19, he fought Anthony Martinez in Aibonito, winning by an eighth round knockout.
José Miguel is undefeated in 22 bouts as a professional, with 15 wins by knockout. He is currently ranked as the number 6 world title challenger in his weight division by the IBF.