From 1990 to 1995 he played minor league baseball in the Cleveland Indians organization.

He was later selected to represent Nuevo León in national amateur baseball competitions and moved to San Antonio, Texas to play baseball at Luther Burbank High School.

In 1994, Flores played for the Charlotte Knights of the International League and in 1995 for the Buffalo Bisons of the American Association.

He spent 14 seasons playing with the Sultanes from 1995 to 2002 and from 2004 to 2009, winning the 1995, 1996 and 2007 Mexican League championships with the Fantasmas grises (Gray Phantoms).

[6][7] He will be enshrined into the Mexican Professional Baseball Hall of Fame as part of the class of 2024.