After retiring as a player, Flores has served as a
manager,
bench coach,
third base coach,
first base coach, and infield coach in the
Puerto Rican Winter League (LBPRC). He managed the
Puerto Rican national baseball team during the Guadalajara 2011 PanAm Games and the 2011 Baseball World Cup. He managed the Cidra Bravos of the FBAPR (PR Baseball Federation), winning back to back national titles during the 2005 and 2006 seasons, and was named manager of the year for 2005. He won his third national title with the club in 2009. Flores managed the 2008
Dominican Summer League Indians, and for five seasons, he worked for the
Chicago Cubs as their infield coordinator. The
Philadelphia Phillies hired Flores to their major league coaching staff for the 2018 season. He was named first base coach and infield coach, and was also in charge of baserunning. In 2019 and 2020, Flores was the
Baltimore Orioles third base coach and infield coach. After he was engaged in a dugout shouting match about defensive positioning by ground-ball relief pitcher
Richard Bleier, Bleier finally played in front of an infield that was not shifted for the final month of the 2019 season, and saw his results improve. In both 2019 and 2020, the team was the American League’s worst defensive infield by the
Statcast metric outs above average. After the 2020 season his contract was not renewed. In December 2021, Flores was named the bench coach of the
Worcester Red Sox, the
Triple-A affiliate of the
Boston Red Sox. On November 22, 2024, Flores was named first base coach of the major-league Red Sox. On April 27, 2026, following the dismissal of manager
Alex Cora and several coaches, Flores was named interim
bench coach. ==References==