For the 2019 regular season, he batted .296/.423/.592 (tied for 8th-highest in Astros history), led the major leagues in walks (119; 6th-most in Astros history) and walk-to-strikeout ratio (1.43), and led the American League in times on base (292; 9th-highest in team history) and Wins Above Replacement ("WAR"; 8.4; second-best in Astros history). Bregman was also 2nd in the AL in on base percentage (.423), 3rd in home runs (41; 7th-most in team history), slugging percentage (.592), and on base plus slugging percentage (1.015), 4th in runs scored (122; 9th-most in Astros history), 5th in RBIs (112), extra base hits (80; 8th-most in Astros history), and sacrifice flies (8), 7th in games played (156), 8th in at-bats-per-strikeout (6.7), and 9th in at-bats-per-home-run (13.5; 10th-best in team history). He swung at the lowest percentage of pitches outside the strike zone of all major league batters (18.8%). He was one of three major league players with at least 100 runs, 100 walks, and 100 RBIs, joining Mike Trout and Juan Soto. He became the only player in Astros history to hit 40 or more homers in a season while striking out fewer than 100 times, and joined Joe Morgan as the only players in team history to amass 100 or more walks and strike out fewer than 90 times in a season. On defense, he played 99 games at third base, and 65 games at shortstop.
In the 2019 postseason, Bregman enjoyed an excellent ALDS against the Tampa Bay Rays, batting .353/.450/.647 with two doubles, one home run, three walks, and two RBIs. Bregman's bat went ice cold in the ALCS and first three games of the World Series, though, as he struggled through a 4-for-31 (.129) slump with only one home run and three RBIs. Bregman broke out of his slump in Game 4 of the World Series by hitting 3-for-5 with a grand slam and 5 RBIs in an 8-1 Astros win that tied the series at 2-2. The Astros eventually lost the series in seven games.
In late 2019, the Houston Astros sign stealing scandal broke, revealing that the Astros had illegally stolen signs using technology in 2017 and 2018. MLB investigated and eventually released its report while punishing the Astros organization. In January 2020, Bregman appeared before the media at the Astros' annual fan festival in Houston that week. He answered repeated attempts by reporters to have him address the scandal with variations of the same phrase: "The commissioner made his report, made his decision, and the Astros made their decision and I have no further comment on it." On February 13, the Astros held a news conference at their spring training facility to address the scandal. Bregman said, "I am really sorry about the choices that were made by my team, by the organization, and by me. I have learned from this and I hope to regain the trust of baseball fans." At that same news conference, Astros owner Jim Crane denied allegations that Bregman and other Astros players wore buzzer devices in 2019, saying, "I truly believe there were no buzzers, ever, and I don't even know where that came from."