Pinto was thrust into action in 2002 against Universidad de Chile's biggest rival, Colo-Colo, when the team's first string goalkeeper was injured and the second string goalkeeper was ejected in the same game. In his first action against Colo-Colo he would hold them scoreless, which would foreshadow his future success against the same team. Pinto would be the team's second team goalkeeper for the 2004 and 2005 season behind Johnny Herrera. Herrera was transferred to Corinthians in 2006 pushing Pinto to become the team's first-choice goalkeeper a position he has held for three years. In 2006 Pinto drew some criticism for his low level of performance. However in 2007 Pinto was named the best player of the year for Universidad de Chile. After a successful 2008 season, Universidad de Chile qualified for the preliminary round of the Copa Libertadores 2009, which would lead to Pinto's first participation in international club football. Universidad de Chile would go on to defeat Pachuca in the preliminary round with Pinto turning in good performances in both games of the two-legged playoff. In the group stage, Pinto would have an incredible performance against Gremio in Porto Alegre making numerous saves in order to maintain a scoreless draw. In the game Pinto received 25 shots from the Brazilian side. Pinto would go on to play in 10 games during the tournament allowing 11 goals, which has led to rumors that Pinto will be making a move to a Mexican club Cruz Azul in mid-2009 for a reported $1.2 million. Pinto won his first title with Universidad de Chile at the end of the Apertura Tournament 2009. In December 2010 after being eliminated of the "Liguilla" for Copa Libertadores 2011 the president of Universidad de Chile Federico Valdés confirmed the transfer of the player to the Mexican club Atlas, in where he will play on loan from La U.
Pinto designs his own goalkeeper jersey, such as former goalkeeper Jose Luis Chilavert. Pinto regularly incorporates a lion or owl into his designs, which are the mascots of Universidad de Chile. Pinto has a twin brother named Juan Francisco. Pinto is also known by his nicknames, Miguelito and Criptonita (kryptonite).