Nicknamed el Pila, Flores currently plays as a midfielder for Alianza after signing a contract with the club starting in the Clausura 2011. He previously played for FAS and Isidro Metapan before joining Alianza. He was named as the most valuable player for the Apertura 2009 final after scoring one goal and leading FAS to its seventeenth title.
On October 2013, he signed with Iraqi team Zakho. During his first season abroad he made twelve appearances and scored four goals for Zakho as they finished in 10th position. Although his stay at Zakho ended once the conclusion of the season due to instability in Iraq, his impact on the field and off field was major that he became a fan favourite.