He went on to win riding titles at Santa Anita Park, Del Mar Racetrack, Oak Tree Racing Association and Fairplex.
Among his notable victories were three Breeders' Cup wins aboard Tempera, Action This Day, and Singletary.
Riding for Godolphin Stables, he won the UAE Derby in 2001 aboard Express Tour.
In May 2007, Flores earned his 3,000th career victory by winning the Lazaro Barrera Memorial Stakes at Hollywood Park Racetrack.
[2] This was effectively reversed by stewards in California on May 7, who ruled following a formal fitness hearing that Flores was permitted to hold a jockey license.