In its history, Comalapa have had 6 managers. The first was the Salvadoran Ricardo Serrano. Serrano was the first Comalapa manager to achieve an honour when, in 2012, the club won the Tercera División. Serrano has the honour of being the club's longest-serving manager having spent two years with the club from 2012 to 2014. Serrano is followed by Uruguayan Pablo Quiñonez who spent one season with the club between 2015 and 2016.