Flores joins the Dolphins after spending 15 years with the New England Patriots organization, where he helped the franchise win four Super Bowls – XXXIX, XLIX, LI and LIII. He spent the past eight seasons (2011-18) coaching defense and seven (2012-18) as a position coach. The Patriots advanced to the AFC Championship game in all seven seasons Flores was a position coach, appeared in four Super Bowls and won three of them.

In 2018, Flores helped the Patriots win Super Bowl LIII in his first season as defensive play-caller. In that game, Flores' defense limited the NFL's second-highest scoring offense to just three points, tying a Super Bowl record. Under his leadership, the defense improved in several categories during the regular season. New England went from 17th in the NFL to seventh in passer rating, allowing opposing passers to compile an 85.4 rating. Much of that was attributed to creating more turnovers, as the Patriots were tied for fifth in the NFL with 28 takeaways and tied for third with 18 interceptions. They ranked 25th and tied for 18th, respectively, in those categories in 2017.

In Flores' three years as linebackers coach (2016-18), the Patriots played in the Super Bowl all three seasons and won two of them. New England had the NFL's best scoring defense (15.6 points allowed per game) in his first year in the role in 2016.

Flores moved to the defensive side of the ball as an assistant in 2011 and was promoted to a position coach in 2012, overseeing the safeties unit from 2012-15. As safeties coach, he helped Devin McCourty earn second-team All-Pro honors in 2013 and was part of a Patriots team that won Super Bowl XLIX at the end of the 2014 season.

In 2010, Flores served as an offensive assistant and also worked with special teams. The Patriots went 14-2 and earned the No. 1 seed in the AFC playoffs. The New England offense led the league in scoring with 32.4 points per game. The unit was fourth with a 5.9 yards per play average and led the NFL with a 109.8 passer rating and a league-low five interceptions. The Patriots' kickoff return unit was among the league's best, ranking fifth with an average starting field position of the 30.0-yard line after kickoffs. The punt return unit was second in the NFL with opponents averaging just 34.2 net yards per punt.

After a four-year playing career at Boston College, Flores joined the Patriots as a scouting assistant in 2004 and was promoted to pro scout in 2006. He then moved into coaching as a coaching assistant for New England from 2008-09.

Flores was a two-year starter at linebacker for Boston College and was part of four bowl-winning teams. He was named to the Big East All-Academic Team in 2003.