Miller made his MLB debut with the Mariners on June 28, 2013. On July 21 he was voted the AL Player of the Week. Miller hit his first grand slam on September 28 in a game in which he hit two home runs. In 76 games, he hit.265/.318/.418, with six triples, eight home runs, 36 runs batted in, and a career-high 13 stolen bases, in 306 at bats. Miller opened the 2014 season as the Mariners' starting shortstop. He was ineffective offensively, hitting just.221/.288/.365, with 10 home runs and 36 RBIs, in 367 at bats, in 123 games. During spring training of 2015, Miller competed with Chris Taylor to become the Mariners' starting shortstop. Taylor broke his wrist during the competition, and Miller became the starter by default. When the Mariners promoted Taylor to the majors in May, they made Taylor the starting shortstop and indicated that Miller would play in a "super utility role", similar to that of Ben Zobrist. On May 17, he won his second AL Player of the Week Award. For the season, Miller hit.258/.329/.402, with 11 home runs and 46 RBIs, in 438 at bats, in 144 games played.
Tampa Bay Rays
On November 5, 2015, the Mariners traded Miller, Logan Morrison, and Danny Farquhar to the Tampa Bay Rays for Nate Karns, C. J. Riefenhauser, and Boog Powell. Midway through the season, Miller made the move from shortstop to first base. He finished his 2016 season batting.243/.304/.482, with career-highs in home runs, RBIs, and runs scored, and was 5th in the AL with six triples, in 548 at bats. After trading Logan Forsythe, the Rays announced that Miller would move to second base for the 2017 season. During the 2017 season, he was the opening day starter at second base, his third main position with the club in one year. On May 16, Miller reported pain in his lower left abdomen, and on May 18 the Rays placed him on the 10-day disabled list. He missed about one third of the 2017 season on the DL due to complications. Miller would play the field predominately to give Tim Beckham the night off, seeing most of his time as the designated hitter, moving the All-Star DHCorey Dickerson to left field. He ended the 2017 season hitting a career-low.201/.327/.337 with 9 home runs and 40 RBIs, in 338 at bats, in 110 games. Miller was designated for assignment by the Rays on June 7, 2018, while hitting.256/.322/.429, with 5 home runs, and 21 RBIs, in 156 at bats.
Milwaukee Brewers
On June 10, 2018, the Rays traded Miller to the Milwaukee Brewers for first baseman/outfielder Ji-man Choi. Miller was optioned to the Triple-A Colorado Springs Sky Soxlater that day, for whom he played eight games. He was designated for assignment on July 28 in order to make room for newly acquired infielder Mike Moustakas on the active roster, and was released on July 31, 2018. With Milwaukee in 2018 he batted.230/.288/.378 with 2 home runs and 8 RBIs in 74 at bats. After Miller was released he had microfracture surgery and right hip labrum surgery to address an injury he had initially suffered in April 2017, and was on crutches for eight weeks.
Cleveland Indians
Miller signed a minor league contract with the Los Angeles Dodgers on February 28, 2019. He opted out of his contract and became a free agent on March 21. Miller signed a major league contract with the Cleveland Indians on March 24. The Indians designated him for assignment on April 15. After clearing waivers, Miller elected free agency on April 17. With Cleveland in 2019 he batted.250/.325/.417 with one home run and four RBIs in 36 at bats.
On April 22, 2019, Miller signed a minor league deal with the New York Yankees. With the Yankees' AAA Scranton/Wilkes-Barre RailRiders in the International League in 2019, he batted.294/.399/.596 with 10 homers and 29 RBIs in 136 at bats in 41 games.
Philadelphia Phillies
Miller was acquired by the Philadelphia Phillies from the New York Yankees for cash considerations on June 13, 2019. In September, Miller became the first Phillies player with three multi-home run games in a nine-game span in team history. Playing for the Phillies in 2019 he batted.263/.331/.610 with 12 home runs and 21 RBIs in 118 at bats, as he appeared in 35 games as a pinch hitter, 19 games at third base, 16 games in left field, and one game each at shortstop, in right field, and as a pinch runner.
St. Louis Cardinals
On February 12, 2020, the St. Louis Cardinals signed Miller to a 1-year contract worth $2 million.