On his 16th birthday in 2007, Flores signed as an international free agent with the New York Mets, and he made his major league debut with them in 2013.

[1] After he turned 13 an agent, impressed with his power, steered him toward the nearby Agua Linda Academy,[1] where he received formal instruction for the first time.

[6] Pitcher Bobby Parnell was placed on the disabled list with a herniated disk in his neck, a roster spot filled by Flores.

[7] He made his debut that day against the Colorado Rockies at Citi Field, going 0-for-4 at the plate and committing an error in the sixth inning, in what would be a 3–2 Mets win.

[8] On August 7, he notched his first career major league hit, a single in the bottom of the second inning off Rockies pitcher Jhoulys Chacín.

In the bottom of the eight inning, he hit a base clearing double off pitcher Manny Corpas for his first three major league RBIs.

Flores started the 2014 season with the Las Vegas 51s in AAA, but was called up April 2 along with Kyle Farnsworth in order to replace Bobby Parnell going to the disabled list and with Daniel Murphy on paternity leave.

The grand slam came in the top of the ninth inning off pitcher Phillippe Aumont with two outs, extending the lead to 11–2.

[25] That same day, Flores hit his first career walk-off, a single, off Phillies' pitcher Elvis Araújo in the bottom of the tenth inning with two outs scoring Juan Lagares for his second RBI of the game.

[26] On July 29, rumors spread during a game against the San Diego Padres that Flores had been traded to the Milwaukee Brewers, along with pitcher Zack Wheeler, for Carlos Gómez.

[27] Despite the rumors, Flores remained in the game, and was visibly emotional when he returned to the field as fans began to give him a standing ovation.

As Flores approached home plate finishing his circle around the bases, he memorably tugged enthusiastically at the "Mets" logo on his uniform front, signifying how happy he was to have remained with the team.

[31][32] After the incident, Flores became a fan-favorite of Mets fans and was given standing ovations in the subsequent weeks, both at home and at away games.

Then, playing against the Chicago Cubs in the NLCS, he batted .286 in four games compiling four hits, one double, one triple, one walk, one stolen base, and striking out two times.

In December, Flores suffered a broken left ankle after being hit by a pitch in winter ball in Venezuela.

[36] On May 12, Flores was put on the 15-day disabled list with a left hamstring injury, with his spot on the roster being taken by Sean Gilmartin.

Flores was batting .180 with one home run and two RBIs in 50 at-bats playing at first, second, and third base filling in as a defensive replacement for Lucas Duda, Neil Walker, and David Wright respectively.

On April 21, the Mets placed Flores on the 10-day disabled list with an infection in his knee which required hospitalization and IV treatment.

[43][44] Flores broke his nose on a foul-tip in the second game of a double-header against the Houston Astros on September 2, which ended his season.

[47] On June 26, Flores drove in the winning run against the Pittsburgh Pirates in the bottom of the 10th inning, giving the Mets a 4–3 victory.

[51] On September 9, Flores hit a home run off of former teammate Jacob deGrom in his return to Citi Field and was met with cheers.

[52] On February 4, 2020, Flores signed a two-year, $6 million contract including a third-year option with the San Francisco Giants.

On August 6, 2024, manager Bob Melvin announced that Flores would miss the remainder of the season after undergoing a Tenex procedure to treat right knee tendinitis.