After two years in the lower levels of their minor league system, Cota was traded with Joe Oliver to the Pittsburgh Pirates for José Guillén and Jeff Sparks on July 23, 1999.

He continued to advance through Pittsburgh's minor league system before making his MLB debut on September 9, 2001.

On April 7, 2003, he caught a perfect game with batterymate John Wasdin of the Nashville Sounds.

[2] He became a free agent at the end of the season and signed a minor league contract with an invitation to spring training with the Cincinnati Reds on February 2, 2009.

On May 24, 2016, he was traded to the Mexican League's Broncos de Reynosa, and then to the Vaqueros Laguna on June 28.