The Yankees promoted Flores to the major leagues on May 29, 2015.[4] On May 30, in his first major league game, he started in left field against the Oakland Athletics.[citation needed] The Yankees optioned Flores to Scranton/Wilkes-Barre on June 10 when Brendan Ryan was activated from the disabled list.[citation needed] On June 21, 2015, the Yankees called Flores back up to cover for the injured Mason Williams
On July 30, 2015, the Yankees traded Flores and José Ramírez to the Seattle Mariners for Dustin Ackley.[5] The Mariners assigned him to the Tacoma Rainiers of the Triple–A Pacific Coast League (PCL). Flores batted .423 in 14 games for Tacoma, before he broke and dislocated his right ankle in August, and missed the remainder of the season.[6]
On November 20, 2015, the Mariners traded Flores to the Milwaukee Brewers for Luis Sardiñas.[7] Flores made the Brewers opening day roster after a strong spring training. On May 21, 2016, Flores homered for the first time off Jacob deGromatCiti Field.
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On November 15, 2016, Flores signed a minor league contract with the Los Angeles Angels organization.[9] He played for the Salt Lake Bees of the PCL, and the Angels promoted him to the major leagues on August 1.[10]
On January 11, 2018, Flores signed a minor league contract with the Arizona Diamondbacks. On March 26, he was traded to the Boston Red Sox.[11] He was released on July 4, 2018.
On July 31, 2019, Flores had his contract purchased by the Minnesota Twins and was assigned to the Triple-ARochester Red Wings.[12] He finished the year batting .308/.435/.449 in 30 games with Rochester. Flores did not play in a game in 2020 due to the cancellation of the minor league season because of the COVID-19 pandemic.[13] He became a free agent on November 2, 2020.
On February 16, 2021, Flores signed a minor league contract with the Washington Nationals organization that included an invitation to spring training. Flores struggled to a .136/.278/.136 slash line with no home runs and 2 RBI in 25 games between the Double-A Harrisburg Senators and the Triple-A Rochester Red Wings and was released by the Nationals organization on July 20.[14]