In 2016, he was moved back to the bullpen, where he said his velocity improved.[7] He began the season with Tampa but was soon promoted to the Trenton Thunder of the Double–AEastern League. On April 26, 2016, Holder pitched the final inning of a joint no hitter that was started by Ronald Herrera.[9] He was an Eastern League Mid-Season All-Star.[8] The Yankees then promoted Holder to the Scranton/Wilkes-Barre RailRiders of the Triple–AInternational League. He struck out 12 batters over four innings on August 28, which earned him Pitcher of the Week honors.[10] He was also named the best relief pitcher and was an organization All-Star, according to MiLB.com.[8][11]
The Yankees promoted Holder to the major leagues on September 2, 2016.[12] His first major league strikeout came against Baltimore Oriolescenter fielderAdam Jones, striking him out on 3 pitches.[13] In 8 appearances with the Yankees to finish 2016, Holder had a 5.40 ERA. On May 5, 2017, Holder got his first major league win pitching a scoreless inning of relief against the Chicago Cubs. In 37 appearances out of the bullpen, Holder finished the 2017 year 1–1 with a 3.89 ERA.
In 2018, Holder made the big league team out of spring training.[14] On August 2, 2018, Holder allowed seven runs without recording an out in a game against the Boston Red Sox. Holder became the second Yankees pitcher to ever post such a line after Bob Kammeyer did so on September 18, 1979.[15] Holder finished the year with a solid 3.14 ERA in 66 innings pitched.
He faltered in 2019, allowing five runs, including a solo homer and a grand slam, without getting an out against the Blue Jays on June 24.[16] After allowing 13 runs and six home runs over his past six outings, he was demoted to Triple-A.[17] The team hoped he could improve his fastball command and the sharpness of his breaking pitches while in the minors.[18] He returned to the majors on July 22, but went down with shoulder inflammation in August.[19][20] He pitched to a 4.98 ERA in 21.2 innings during the 2020 season.[21] On December 2, 2020, Holder was non-tendered by the Yankees.[22]
On December 17, 2020, Holder signed a one-year, $750,000 contract with the Chicago Cubs.[23] He was placed on the injured list on April 1 because of a right shoulder strain.[24] On April 26, 2021, Holder was moved to the 60-day injured list.[25] He did not appear in a game for Chicago due to the injury and was outrighted off of the 40-man roster on November 3, 2021.[26] He elected free agency the following day, but re-signed with the team on a minor league contract on November 19.[27]
Holder went into 2022 as a non-roster invitee.[28] He was reassigned to the minors on April 4.[29] After starting the year on the injured list, Holder was again transferred to the 60-day injured list in May. Following a rehab assignment with the rookie–level Arizona Complex League Cubs, he was finally activated on August 4.[8] He then spent the remainder of the season with the Triple–A Iowa Cubs, making 14 appearances and struggling to a 10.00 ERA with 19 strikeouts in 18.0 innings pitched. He elected free agency following the season on November 10, 2022.[30]
On November 29, 2022, Holder signed a minor league deal with the Los Angeles Angels.[31] He competed in spring training but was reassigned to minor league camp on March 22, 2023.[32] In 46 appearances for the Triple–A Salt Lake Bees, Holder recorded a 5.40 ERA with 76 strikeouts and 2 saves across 66+2⁄3 innings of work. He elected free agency following the season on November 6.[33]