In 2006, Pérez was a player-coach for the Double-A Mississippi Braves.
Atlanta Braves manager Bobby Cox named Pérez as his bullpen coach for the 2007 season.
When Fredi Gonzalez was named the Braves manager for the 2011 season, he retained Pérez as his bullpen coach.
After the Braves fired Gonzalez he was moved to be the current first base coach for the new manager Brian Snitker.

Pérez was hired as the manager for the Águilas del Zulia of the Venezuelan Winter League for two seasons, 2008-2010.
He rejoined the team in the 2014 season.
In 2015, Pérez managed the Tigres de Aragua.
In 2006, Pérez was a player-coach for the Double-A Mississippi Braves. Atlanta Braves manager Bobby Cox named Pérez as his bullpen coach for the 2007 season. When Fredi Gonzalez was named the Braves manager for the 2011 season, he retained Pérez as his bullpen coach. After the Braves fired Gonzalez he was moved to be the current first base coach for the new manager Brian Snitker.
Pérez was hired as the manager for the Águilas del Zulia of the Venezuelan Winter League for two seasons, 2008-2010. He rejoined the team in the 2014 season. In 2015, Pérez managed the Tigres de Aragua.
Eddie Pérez (baseball)