On June 10, 2007, FMF General Secretary Decio de Maria revealed the groups for the upcoming tournament.
This is the first time they are taking part in a Primera División tournament since they were relegated after Clausura 2005.
Atlante made the move to Cancún, Quintana Roo, and played in the Estadio Andrés Quintana Roo after having played in Estádio Azteca for over a decade.
At their new home, on December 9, 2007 Atlante won the Apertura 2007 by defeating UNAM 2–1 on aggregate.
By being the Apertura 2007 runner-up, the Pumas earned a berth in the 2008–09 CONCACAF Champions League Preliminary Round.