Emilio came through the youth system at Uruguay’s most successful club, C.A. Peñarol, and was promoted to the first team in the 2010-11 Primera División season, for which he was assigned squad number 2. He made seven appearances in this season, one of which was as a substitute. His debut came in a 2-0 win against Cerro on 13 March 2011.
Emilio was also a squad member for Peñarol’s 2011 Copa Libertadores campaign, in which the club reached the final. He was an unused substitute in six 2011 Libertadores matches, including the first leg of the final against Santos of Brazil.