Flores debuted with the A Ball Kingsport Mets in 2008. He moved on to play eight games with Brooklyn Cyclones that year as well as with the Savannah Sand Gnats. While in the Appalachian League he was one of the toughest hitters to strike out & ranked the circuit's #2 prospect.
In 2009 he led all short stops in fielding & started at second base in the Futures Game.
Flores played the next three seasons with the A ball St. Lucie Mets, hitting .300 in 2010. He began 2012 in St. Lucie & was moved up to the AA Binghamton Mets, where he hit .311 in 66 games. In 2013 he was one of the Mets top prospects & started out the year at AAA Las Vegas. There he had a fine season hitting .321 with 15 HRs 36 doubles & 86 RBIs.
On his 22nd birthday he was brought up to the Mets big league squad debuting on August 6th. The next day he was the hitting star in Matt Harvey's four hit shut out of the Colrado Rockies at Citi Field. Flores had two hits including a bases loaded, base clearing double in the 8th inning.
Flores drove in runs in the next five games as well with another three RBI day on August 10th in a 4-1 Mets win. The next day he hit his first career HR, it came in Arizona in a 9-5 win over the D-backs.
Flores hot start tailed off as he finished up the year batting .211 with one HR, 5 doubles & 13 RBIs
Flores began 2014 with the Mets, going 0-4 in the second game of the year. He was sent back to AAA Las Vegas, returning on May 9th. He hit safely in five of his first six games, getting named the club's main short stop by manager Terry Collins, in place of a struggling Ruben Tejada.
On June 2nd, Flores had his biggest day at the plate in the big leagues, in an 11-2 Mets win at Philadelphia. Tejada began it with a two run double in the 6th inning & finished it up with a grand slam HR off Phillipe Aumont in the 9th inning.
He didn't hit much the rest of the month & lost the starting short stop role. He was batting .225 on June 25th when he was sent back down to AAA Las Vegas. There he hit real well, hitting in 22 consecutive games keeping his AAA average at .323 on the seasons. He was called back up to the big league club on July 24th & got a hit in his return.
On August 2nd he drove in two runs in the Mets 3-2 win over the San Francisco Giants. On September 16th he had one of his biggest days, collecting three hits with two HRs & six RBIs in a 9-1 Mets win over the Marlins at Citi Field. For 2014 he batted .251 with 6 HRs 13 doubles & 29 RBIs.
In the 2015 off season, there was a lot of talk for the Mets to get a short stop. Many names & rumors were thrown around bit no deals were made. Manager Terry Collins announced Flores was to be the teams short stop even though he was not familiar with the position. He handled it well, dismissing the negative press against him & the rumors of trades.
Although he struggled on the field, making 10 error in 69 games at short, he started off the season hitting well. In mid April he hit three HRs over a six game span. On April 16th, his three run HR helped the Mets to a 7-5 win over the Miami Marlins. Two days later his two run blast helped the team in a 5-4 victory. On April 22nd, his two run HR helped beat the Atlanta Braves 3-2 also at Citi.
In mid May he had a similar stretch, On May 16th he hit a grand slam HR while batting in the 8th position being the first player to do that in an NL Park. Pitcher Jacob deGrom batted 8th & had three hits.
On May 25th his 6th inning HR off the Phillies Elvis DeFratus breaking a 3-3 tie in what turned out to be the game winner. The next night he tied up a game with a sac fly & then hit a game winning walk off single to win it. Although his average never went higher than the .250s he had ten HRs by mid June. But from there he would not hit another through the end of July.
On July 29th, In a snowballing social media frenzy, it was reported that the Mets had traded Flores to the Milwaukee Brewers along with Zack Wheeler in exchange for former Met Carlos Gomez of the Milwaukee Brewers. When Flores came to bat the fans gave him a standing ovation & began shouting to him that he had been traded.
When he took the field in the top of the inning, the young Flores began to shed tears in a very emotional scene. It was a strange sad emotional scene for the young man who had been in the Mets organization since he was 16 years old.
Then later in the 9th inning, Manager Terry Collins was seen talking to Flores in the dugout as he removed him from the game.
Mets Captain David Wright, Veteran Michael Cuddyer & Flores' friend Ruben Tejada followed Wilmer into the run way to support him & calm him down. After the game Manager Terry Collins was upset in his press conference, saying he knew nothing about a deal being made. He said all he knew was he had a game to play & a game to try to win.
After the game, GM Sandy Alderson also reported that no deal was going to happen. It was a bizarre night at Citi Field for sure as the Mets lost 7-3 to the San Diego Padres. The deal did not go through, as the Mets siad they were concerned about Gomez' medical report, most importantly a former hip injury.
The aftermath surrounding the incident was incredible. The media were all over the Mets organization for the debacle & the Mets fans took Flores side, as did all of America. He soon became Citi field's sweetheart.
New Yorkers began to sympathize with Flores, and in this sensitive world we live in, the statement was it's ok to let your emotions out at work, on the field & publicly. It also showed how much Flores wanted to be a part of the Mets & what's happening with this team. The fans fell in love with him & he was to be a Mets cult hero forever.
After a devastating loss the next day, blowing a 7-1 lead in two rain delays the second place Mets hosted the first place Washington Nats.
Flores responded by driving in the Mets first run of the night & then hit an incredible exciting walk off HR in the bottom of the 12th inning. It was his first career walk off & Flores was the hero of the night. In the words of Mets manager "you can't write that"!
As August started all the Mets licked in gear & hit like a machine. Flores hit doubles in three straight games during the Mets seven game win streak. In mid August he drove in runs in five straight games, as the Mets won seven of eight on a very successful road trip through Baltimore, Colorado & Philadelphia. Flores collected 13 hits with ten RBIs in that stretch.
On August 24th, as Mets Captain David Wright made a triumphant return after being down with injury since April. That night the Mets clobbered the Phillies in Philadelphia 16-7, Flores had another huge night. He collected three hits with two HRs & a season high five runs driven in. In the 4th inning he blasted a two run HR then a three run shot in the 5th inning.
In early September Flores hit HRs in back to back games in Miami but cooled off for the rest of the regular season. He completed the season batting .263 with 16 HRs 22 doubles 59 RBIs 55 runs scored & a .295 on base % in 137 games. Flores would play 103 games at short stop & 37 games at second base.
2016 NLDS: Flores made his first appearance in Game #2 of the NLDS against the Los Angles Dodgers, after Ruben Tejada was taking out of the game after getting slid into by Chase Utley. Flores would be the Mets short stop the rest of the way.In one at bat he went 0-1.
In Game #3 at Citi Field, Flores had two hits & scored two runs in the Mets 13-7 victory. He would get just one hit in six at bats in the next two games with one walk.
2016 NLCS: In the Mets NLCS sweep of the Chicago Cubs, Flores collected four hits, two of them coming in the fourth & final game. He did not score any runs but did draw one walk.
2016 World Series: In the World Series loss to the Kansas City Royals, he had his troubles as did many other Mets players. Flores went 1-17 with a walk. Overall in the post season he batted just .195.
Trivia: Flores appeared on the Jimmy Kimmel Show with David Wright, Matt Harvey & Jacob deGrom when the Mets won the NL pennant.
During the off season, the Mets acquired Neil Walker to play second base & Asdrubal Cabrera to play short stop. Ruben Tejada was gone so Flores looked to be everyone's back up including an aging, hurting David Wright at third base.
But Flores struggled, missing a lot of action due to injury in May & not getting over the .200 batting mark until June. He did not get his first HR until the last day of April & didn't hit another until mid June.
On June 15th Flores had his best day of the season until that point, collecting two hits including a two run HR his second of the year. He drove in four runs in the Mets much needed 11-1 win over the Pittsburgh Pirates. By this time Flores was seeing more time at third base as David Wright underwent neck surgery.
Through mid June 2016, in his four year career Flores is batting .253 with 237 hits 5 HRs 46 doubles 110 RBIs 102 runs scored & a .290 on base %.