Naquin played for the Carolina Mudcats of the High-ACarolina League and the Akron Aeros of the Double-AEastern League in 2013, hitting a combined .269 with ten home runs, 48 RBIs, and 15 stolen bases in 126 total games between both teams. After the 2013 season, the Indians assigned Naquin to the Arizona Fall League, and he participated in the Fall Stars Game.[10] Naquin began the 2014 season with Akron, but suffered a broken hand in July.[11] He required surgery, and missed the remainder of the 2014 season. In 76 games for Akron before his injury, he was batting .313 with four home runs and 30 RBIs. Naquin began the 2015 season with Akron.[12] In June, the Indians promoted him to the Columbus Clippers of the Triple-AInternational League.[13] However, a concussion and soreness in his right hip limited him to 50 games played with Columbus.[14] In 84 games between Akron and Columbus, he slashed .300/.381/.446 with seven home runs and 27 RBIs. After the 2015 season, the Indians added Naquin to their 40-man roster.[15]
Naquin began 2017 with Cleveland. However, he was hampered with injuries and struggled with the Indians, and he only appeared in 19 games for Cleveland in which he hit .216. He spent the majority of the year with Columbus, where he slashed .298/.359/.475 with ten home runs and 51 RBIs in 80 games.[21] He played in 61 games for the Indians in 2018, hitting .264/.295/.356 with 3 home runs and 23 RBI.
In 2019 with Cleveland, Naquin played in 89 games, slashing .288/.325/.467 with 10 home runs, 34 RBI, and 4 stolen bases.[22] Overall with the 2020 Cleveland Indians, Naquin batted .218 with four home runs and 20 RBIs in 40 games.[23] Naquin was not tendered a contract for the 2021 season by the December 2, 2020, deadline, making him a free agent.[24]
Cincinnati Reds
On February 18, 2021, Naquin signed a minor league contract with the Cincinnati Reds organization that included an invitation to spring training.[25] On March 29, 2021, Naquin was selected to the 40-man roster.[26]
Naquin appeared in 127 games with Cincinnati in 2021, finishing with a .270 batting average, 19 home runs, and 70 RBIs.[27]
In 2022, Naquin appeared in 56 games for Cincinnati, posting a batting line of .246/.305/.444 with 7 home runs and 33 RBI.
New York Mets
On July 28, 2022, the Reds traded Naquin and Phillip Diehl to the New York Mets for minor league prospects Jose Acuña and Hector Rodríguez.[28] He played in 49 games for the Mets down the stretch, slashing .203/.246/.390 with four home runs and 13 RBIs.
Milwaukee Brewers
On February 21, 2023, Naquin signed a minor league contract with the Milwaukee Brewers organization.[29] In 40 games for the Triple–A Nashville Sounds, he hit .284/.333/.432 with 6 home runs and 21 RBI.[30]
Chicago White Sox
On August 7, 2023, Naquin was traded to the Chicago White Sox in exchange for cash considerations.[31] In 28 games for the Triple–A Charlotte Knights, he batted .217/.294/.371 with 3 home runs and 9 RBI. On September 26, 2023, the White Sox selected Naquin's contract to the major league roster after Luis Robert Jr. suffered an injury.[32] Appearing in 5 games for Chicago, he went hitless in 8 at-bats. Naquin was released by the White Sox on October 3 following the waiver claim of Alex Speas.[33]