Three times Nick Markakis came up with bases loaded Friday night, and not once did the Braves’ cleanup hitter come through.

Markakis grounded into an inning-ending double play with the bases loaded in the ninth as the Mets held on for a 5-3 win to open a three-game series at Citi Field.

“I don’t know if that’s happened to me,” said Markakis, who went 0-for-5, left nine runners on base, and twice grounded into double plays with bases loaded. “Just some bad at-bats by me today, especially in some big situations. Second-guessing myself up there a couple of times.

“You’ve got to kind of eliminate the mental aspect of it; I was thinking up there too much. You get yourself into trouble when you do that.”

Markakis came in with a .305 overall batting average, but with bases loaded he’s now 0-for-7 with no RBIs this season.

The Mets didn’t have a hit with a runner in scoring position until the seventh inning against the Braves, but it didn’t much matter, since two of their first three hits sailed over the outfield fence.

Braves starter Alex Wood allowed as many home runs (two) in the first four innings as he had all season.

It was the seventh loss in 10 games for the Braves (29-32), who slipped to 3 ½ games behind the National League East-leading Mets. The Braves have lost 12 of 17 games between the teams going back to July 7.

The Braves made things interesting, for sure, in the ninth, after a Jace Peterson walk and Cameron Maybin single brought career Mets nemesis Freddie Freeman to the plate with one out against closer Jeurys Familia. He took some mighty cuts and fouled off a few pitches before drawing a walk that loaded the bases once again for Markakis.

“I thought Free put up one heckuva at-bat against him,” Braves manager Fredi Gonzalez said. “With Nicky, I felt pretty good. Not that he’s going to run the ball out of the ballpark; I thought he was going to split a game, get at least two guys in.”

Instead, for the second time Friday he grounded into a bases-loaded, 4-6-3 double play, this one a game-ender. Markakis also grounded into a double play in the seventh with none out, after Alex Torres had issued consecutive walks to Maybin and Freeman and was clearly having trouble finding the plate.

“I have a plan going up there,” Markakis said. “You change your thought process in the middle of it, it can really hurt you. It got me tonight. Swung at a bad pitch from Torres with the bases loaded, after him walking a couple of guys. I should have been looking for a ball over the plate, instead I was trying to do too much. It came back to bite me today.

“And the last time, in that last inning, I was just looking for a good pitch. I got a good pitch; sometimes it’s hard to hit 99 (mph). I gave it my shot, and we failed, or I failed. We move on, I move on, and we look to win the game tomorrow.”

One run scored when he grounded into a double play in the seventh to cut the lead to 4-3, and Juan Uribe grounded out to the pitcher to end the inning. The Braves were 2-for-12 with runners in scoring position.

The Mets cushioned their lead with a run in the seventh on two hits, including Michael Cuddyer’s two-out double off reliever David Aardsma.

Wood (4-4) was charged with six hits and five runs (four earned) in 6 1/3 innings, with four walks and six strikeouts. The fourth run he allowed was unearned after Wood’s errant pickoff throw at second base in the sixth inning. The left-hander tried to catch Mayberry off guard, but the throw sailed past second baseman Peterson into center field, moving runners to second and third and allowing Eric Campbell’s groundout to move the lead back to two runs, 4-2.

After the Mets took a 3-0 lead on Wilmer Flores’ leadoff homer in the second inning and John Mayberry Jr.’s two-run homer in the fourth, the Braves scored twice in the fifth to cut the lead to 3-2. But they let ancient starter Bartolo Colon (9-4) off the ropes in that inning when they didn’t score again despite having two in scoring position with one out.

Colon, 42, who had a 6.44 ERA in his previous five starts, limited the Braves to six hits and two runs in six innings and improved to 3-0 in three starts against them this season. He had two walks (both intentional) and three strikeouts Friday, and has issued just one other walk in six starts (41 innings ) against the Braves over two seasons.

Wood was six years old when Colon began his career in 1997.

“He’s tough on us,” Gonzalez said of the stocky right-hander, who’s 4-2 with a 3.07 ERA in his past six starts against the Braves. “He throws the ball over the plate and the ball goes everywhere – it cuts, it sinks, it rises. We’ll try to figure him out.”

The Braves also failed to score after Uribe’s leadoff double in the sixth, when A.J. Pierzynski followed by popping out and Jonny Gomes struck out. Colon intentionally walked Andrelton Simmons to bring up Wood, and the Braves weren’t about to pinch-hit for him in the sixth inning of a one-run game, not with his pitch count low at that point (74) and given the well-documented struggles of their majors-worst bullpen.

Wood tried to sneak a two-out bunt for a base hit, and nearly did it, the ball rolling an inch or so foul just before it stopping rolling up the third-base line. He ended the inning with a comebacker to Colon.

Mayberry’s homer off Wood with one out in the fourth inning came on a 90-mph fastball with the count 2-1, and Flores’ second-inning homer came on an 88-mph fastball with a 1-1 count. Mayberry also walked and singled in the sixth inning, and has six hits and two homers in 15 career at-bats against Wood.

Colon had faced two batters over the minimum through four innings, allowing only a single and hit batsman in that span, before the Braves opened up the fifth with three consecutive singles by Pierzynski, Gomes and Simmons. Wood hit a potential double-play grounder to shortstop Flores, who dropped it and had to settle for one out at second base, with the Braves’ first run scoring on the play.

Peterson followed with an RBI double to the base of the right-field wall to cut the lead to 3-2, and the Braves still had two runners in scoring position (Wood was held up at third base on Peterson’s double). Maybin struck out, and Colon intentionally walked Freeman to bring up Markakis with bases loaded and two out.

Markakis hit a comebacker to Colon to end the inning and strand three in what was then a one-run game.