Cooney made his major league debut on April 30, 2015, replacing the injured Adam Wainwright in the Cardinals' starting rotation.[11] Cooney struggled in his debut, and was optioned back to Memphis the next day.[12] On May 17, he was named the PCL Pitcher of the Week after allowing a 0.66 ERA in 13+1⁄3 IP against the New Orleans Zephyrs and Omaha Storm Chasers. He also held batters to a .143 batting average against (7-for-49).[13] In his first 14 starts of the season with Memphis, Cooney completed 88+2⁄3 IP, allowing 27 ER for a 2.74 ERA. He also struck out 63 batters and was 6–4 in won–loss decisions. He was named to the 2015 PCL All-Star squad on July 1.[8] The Cardinals recalled him the next day when they placed outfielderJon Jay on the disabled list.[14]
On July 24 against the Atlanta Braves, Cooney earned his first major league victory by pitching a career-high seven innings in a 4−2 outcome. He had previously received no-decisions in each of his first five major league starts. Further, he had a 12-inning scoreless streak that ended in the sixth inning.[15] The Cardinals withheld Cooney from play for the remainder of the season starting on September 1 due to appendicitis. His major league totals for the season included a 1–0 record, 3.16 ERA, 28 hits, 10 walks allowed and 29 strikeouts in 31+1⁄3 innings.[16]
Prior to the 2016 season, Baseball America rated Cooney as the second-best prospect in the Cardinals organization.[17] However, Cooney missed the whole 2016 season due to a shoulder injury.[18]
Cleveland Indians
On November 18, 2016, Cooney was claimed off waivers by the Cleveland Indians.[19] The Indians released Cooney on April 2, 2017.[20] Cooney signed a minor league deal with the Indians on April 6, 2017.[21] He pitched only four games in 2017, with the AZL Indians where he posted a 6.00 ERA, due to injury.[22] He elected free agency following the season on November 6.[23]