Despite being below .500 (60–62) as late as August 19, the Mets went 27–13 in their final 40 games to make the postseason in consecutive seasons for the second time in franchise history.

Following a narrow Opening Day defeat, the Mets split the series in Kansas City behind a scoreless outing by Noah Syndergaard and a two-run home run by Neil Walker.

On May 27, the Mets returned to Citi Field to play the Los Angeles Dodgers in what was the first game in a 1986 World Championship 30th Anniversary Weekend Celebration.

The Mets continued to struggle in June, in part due to an offense not producing many runs, in particular with runners in scoring position.

While Bartolo Colón and Noah Syndergaard continued to pitch well, Steven Matz, Jacob deGrom and Matt Harvey would not win a game in June.

Duda would be replaced by James Loney, and the Mets brought back former shortstop José Reyes to fill in for Wright at third base.

At the end of the month, following a sweep at the hands of the Nationals, it was announced that both Steven Matz and Noah Syndergaard had been pitching with bone spurs in their throwing arms.

The Mets returned home to Citi Field to start the month and swept a four-game series from the Chicago Cubs, similar to what they had done in the 2015 NLCS.

José Reyes would return to the Mets on July 5, just in time for a pivotal four game series with the divisional rival Washington Nationals before the All-Star Break.

The following day, it was announced that Bartolo Colón had been selected to replace Madison Bumgarner in the 2016 MLB All-Star Game, joining teammates Noah Syndergaard, Jeurys Familia and Yoenis Céspedes.

After the All-Star Break, Jacob deGrom pitched arguably the best game of his young career, as he dominated the Phillies in a complete-game shutout, while striking out 7 batters.

In August, Sandy Alderson would come through with a deal at the trade deadline, as he acquired outfielder Jay Bruce from the Cincinnati Reds in exchange for second baseman Dilson Herrera and pitching prospect Max Wotell.

To make matters worse, star outfielder Yoenis Céspedes, who undoubtedly had been the best hitter on the team, was diagnosed with strained right quadriceps, and was placed on the 15-day DL.

The Mets would also lose second baseman Neil Walker for the season after he required surgery to fix a herniated disc in his back.

Heading into the final month of the regular season, the Mets remained in a race for a Wild-Card spot along with the Marlins, the San Francisco Giants, and the St. Louis Cardinals.

It was later revealed that these struggles were injury related, and deGrom underwent season-ending surgery on his ulnar nerve in order to relieve discomfort in his elbow and numbness in his fingers which had plagued him during the season.

Fortunately for the Mets, Noah Syndergaard and Bartolo Colón managed to stay healthy throughout the entire season, and minor leaguers Seth Lugo and Robert Gsellman would provide great starts while filling in for the injured stars down the stretch, helping guide the Mets to multiple series wins throughout the final month.

Later on in the home stand, after the Mets were swept by the visiting rival Atlanta Braves, New York began a four-game series against the Phillies with a 9–8 win in 11 innings.

The Phillies held a 6–4 lead heading into the bottom of the 9th, and with the Mets down to their final strike, José Reyes hit a game-tying two-run home run to send the game to extra innings.

After this, the Mets took two of three in Miami before heading to Philadelphia to end the season, needing to win the series in order to qualify for a Wild Card spot.

The Mets played the San Francisco Giants in the National League Wild Card Game at Citi Field on October 5, 2016, which was presented on ESPN.