He left Luis Ángel Firpo for San Salvador FC in 2002, losing the final of the Apertura 2002 but winning the Clausura 2003.
He rejoined Isidro Metapán in 2009, after two short-lived spells at Atlético Balboa (2008) and Nejapa (2009), to win another league title in the Clausura 2010 with the Santa Ana team.
Alfaro was ranked number 8 in the World's Most Successful Goalscoring Goalkeepers of All Time, chart with 31 goals, with 11 of those coming from a penalty kick.
After his retirement from football, Misael Alfaro decided to try his luck in the technical staff of different national teams as goalkeeper coach.
In 2015 Alfaro was announced as new goalkeeper coach of Luis Ángel Firpo, team that at that time played in the Segunda División.
Alfaro made his debut for El Salvador in an April 1991 UNCAF Nations Cup qualification match against Nicaragua, and has earned a total of 42 caps, scoring no goals.