The club was first affiliated to the AFA in 1954, but was desafiliated ten years after. Muñiz returned to play the AFA tournaments in 1979 and in 1981 gained its first promotion to Primera C Metropolitana. The only title Muñiz obtained was the 1986-87 Primera D Metropolitana championship.
Muñiz has been disafilliated for a total of 7 times (1964, 1990–91, 1994–95, 2001–02, 2005–06, 2007–08 and most recently in 2010-11 season). Once the punishment finished, the squad was able to return for the 2011-12 tournament.