In the NLDS against the Los Angeles Dodgers, Flores hit .300 in four games compiling 3 hits, 1 double, 2 walks, 2 runs scored, and striking out 4 times. Then, playing against the Chicago Cubs in the NLCS, he batted .286 in four games compiling 4 hits, 1 double, 1 triple, 1 walk, 1 stolen base, and striking out 2 times. During the series against the Dodgers, Mets' shortstop Ruben Tejada was injured by the Dodgers' Chase Utley. The injury occurred with a controversial slide, thought dirty by many, and resulted in a broken leg for Tejada. Flores played shortstop for the remainder of the postseason. Once he moved to the more important defensive position, Flores played fine defense, but struggled hitting. He was the last out of the World Series, striking out looking in game five against Kansas City Royals closer Wade Davis, to clinch the series for the Royals. Flores appeared in all five games, batting .059 with 1 hit, 2 runs scored, 2 walks, and 3 strikeouts.