After signing, the Yankees assigned Holder to the Staten Island Yankees, where he spent the whole season. Holder played for the Charleston RiverDogs in 2016, where he batted .290 with one home run and 18 RBIS, and the Tampa Yankees in 2017 where he batted .271 with four home runs and 44 RBIs.
In 2017, Holder was named as the Best Defensive Shortstop in the minor leagues.[6] Holder was invited to the Arizona Fall League in 2017 and hit .333 over 45 at bats.[7] He was then a non-roster invitee for the New York Yankees spring training in 2018 and started the year with Trenton Thunder.[8] He also spent time during the season with the Charleston RiverDogs and the Trenton Thunder. Over 48 games between the two teams, he hit .257 with three home runs.
The Yankees invited Holder to spring training as a non-roster player in 2019.[9] He spent the year with Trenton, slashing .265/.336/.405 with nine home runs and forty RBIs over 112 games.
On December 10, 2020, Holder was selected by the Philadelphia Phillies in the Rule 5 Draft.[10] On January 30, 2021, Holder was traded to the Cincinnati Reds in exchange for cash considerations.[11] On March 30, 2021, Holder was returned to the Yankees.[12]
Colorado Rockies
On December 16, 2021, Holder signed a minor league contract with the Colorado Rockies.[13] He was released on July 24, 2022.