After missing the playoffs for three consecutive tournaments, Morelia finished in third place in the general table in the Apertura 2009. Morelia defeated Santos Laguna in the first round, 4–2 on aggregate. Morelia was then defeated by Cruz Azul in a semi-final that was filled with controversy due to Cruz Azul player Joel Huiqui intentionally using his hand to hit the ball away and prevent Morelia midfielder Wilson Tíago from scoring. (Huiqui later played for Morelia.) With a 2–1 aggregate score, Morelia was eliminated. Morelia qualified for the 2010 Copa Libertadores by ending in third place in the classification phase. It was the second time that Morelia participated in the Copa Libertadores, the first being in 2002. Morelia was the Runner-up of the Clausura 2011, after a hard-fought final against Pumas. Pumas won the tie 3–2 on aggregate, taking the trophy home.