' scouts Daraka Shaheed and Joe Siers, who watched Quintana pitch in the FSL the previous season, recommended that the team sign him. Quintana signed with the White Sox, receiving a major league contract, on November 10, 2011. The White Sox assigned Quintana to the Birmingham Barons of the Class AASouthern League. After starting the season with a 1–2 win-loss record, a 3.06 ERA, and 26 strikeouts in 35 innings pitched for Birmingham, the White Sox promoted Quintana to the majors on May 7, 2012, according to a new MLB rule that allow teams to carry a 26th man on their 25-man roster during the day of a doubleheader; the White Sox returned Quintana to Birmingham after the games. He made his MLB debut in the first game of the doubleheader, pitching innings in relief, allowing no runs, one hit, and two walks while striking out three. Quintana was optioned back to Birmingham the next day, and he stayed there up until May 24, when he was promoted to the Charlotte Knights of the Class AAAInternational League. However, he did not pitch there, as he was promoted to Chicago the next day when John Danks was placed on the 15-day DL. On May 25, 2012, Quintana got his first Major League victory during a 9–3 victory over the Cleveland Indians pitching six innings giving up two runs on four hits, walking three and striking out four. During a game against the Tampa Bay Rays on May 30, 2012, Quintana was ejected by umpire Mark Wegner after throwing a pitch behind Ben Zobrist. During the 2012 year, Quintana appeared in 25 games making 22 starts going 6–6 with a 3.76 ERA. In 2013, Quintana pitched 200 innings in 33 starts, going 9–7 with 164 strikeouts and a 3.51 ERA. His 17 no decisions were the most among MLB starting pitchers in 2013. On March 24, 2014, Quintana signed a five-year extension with the White Sox, which also includes club options for a further two years. He qualified as a "Super 2" arbitration eligible player after the 2014 season, activating a clause in his contract making the deal worth a guaranteed $26.5 million. During the 2014 year, Quintana made 32 starts going 9–11 with 178 strikeouts and a 3.32 ERA in 200⅓ innings. He followed up with a 3.36 ERA and 9–10 record with 177 strikeouts in innings in 2015. That season he led all major league pitchers in curveball percentage. Through the All-Star break in 2016, Quintana pitched to a 7–8 record with a 3.21 ERA in innings pitched. He was named to the MLB All-Star Game as an injury replacement for Danny Salazar. He finished the season 13–12 with a 3.20 ERA, striking out 181 batters while making 32 starts. Quintana finished tied for tenth in the voting for the American League Cy Young Award with Michael Fulmer, receiving one fifth place vote. Quintana pitched for the Colombian national baseball team in the 2017 World Baseball Classic. The White Sox named him their Opening Day starting pitcher for the 2017 season.
Chicago Cubs
On July 13, 2017, the White Sox traded Quintana to the Chicago Cubs for prospects Eloy Jiménez, Dylan Cease, Matt Rose, and Bryant Flete. He made his first start for the Cubs on July 16, striking out twelve in an 8–0 victory against the Baltimore Orioles. Quintana struggled in August, but had a 2.51 ERA in five starts in September. Quintana had a 13–11 record and a 4.03 ERA in 32 starts for the Cubs in 2018. He started the 2018 National League Central tie-breaker game. After the season, the Cubs exercised their $10.5 million contract option on Quintana for the 2019 season. Quintana pitched to a 4-1 record with a 2.02 ERA for the month of August 2019. In July 2020, Quintana underwent surgery to repair a lacerated nerve on his thumb on his throwing arm, which he incurred while washing dishes.