In 2003, he was signed by the Brampton Hitmen of the Canadian Professional Soccer League. He scored his first goal for the organization on July 4, 2003 in a 2-0 victory over Toronto Croatia. He helped Brampton by finishing second in the Western Conference and thus securing a postseason berth.
In the quarterfinals the Hitmen faced Toronto Croatia, and Flores scored the equalizing goal to conclude the match to a 1-1 draw.
The game went into penalties with Toronto winning 4-3 in the shootout. After Toronto Croatia was caught fielding a illegal player the league reversed the result and Brampton advanced to the next round.
Brampton"s next opponents would end up being London City, where once again the match went into penalties with Flores contributing a successful penalty kick, and the match concluding in a 5-3 victory. He featured in CPSL Championship match against Vaughan Sun Devils coming on as a substitute for team captain Philosophy Ionadi.
Brampton would end up winning the match by a score of 1-0, thus marking the franchise"s first Championship.
Flores retired from competitive soccer after the 2003 season and served as a Ontario Soccer Association Provincial and Regional Head Coach from 2005 till 2011. In 2011, he was appointed Technical Director Guelph Soccer. In 2012 he served as assistant coach under Brett Mosen for Hamilton Rage of the Premier Development League.
On February 26, 2013 he was appointed the first head coach for K-West United for the USL West-League.
After a controversy regarding his professional soccer resume, Flores was dismissed from his post of head coach. On May 22, 2014, he was named the head coach for the Cayman Islands women"s national football team