Mosquera began his youth career with Centauros Villavicencio and made his first team debut with the club in 2006. After two seasons with Centauros he signed with Primera A club Deportes Quindío and remained at the club until 2010. Mosquera quickly established himself as a first team starter for Quindío. For the second half of the 2010 season he was sent on loan to La Equidad. Mosquera continued as a regular starter for his new club and also played for La Equidad in the 2011 Copa Sudamericana. On August 19, 2011 he helped lead his club to a 2-0 victory over Peru’s Juan Aurich, scoring the games opening goal in the Copa Sudamericana match.
In January 2012 it was reported that Mosquera was close to signing with top Colombian club Millonarios, however Mosquera decided against the offer and began negotiating to join a club in Major League Soccer (MLS). The Portland Timbers of MLS announced the signing of Mosquera on January 17, 2012.
Mosquera was released by Portland on May 15, 2013.