From 1998 to 2006, Morales played for four different clubs in the Argentine Primera División, including two stints each with Lanús and Arsenal de Sarandí.

In August 2007, Morales moved to the United States to play for Real Salt Lake of Major League Soccer.

Morales was acquired by Real Salt Lake at the same time as fellow Argentines Matias Mantilla and Fabián Espíndola.

[2] He started 29 of Real Salt Lake's 30 contests, totaling 6 goals (tied with Robbie Findley for second-highest on the team, just behind Yura Movsisyan).

[citation needed] It was the second-highest total in the MLS that season, behind only league MVP Guillermo Barros Schelotto of the Columbus Crew.

Morales announced that he would leave Real Salt Lake on November 3, 2016, having tallied more assists than any player in club history.