The Boston Red Sox signed Margot as an international free agent from the Dominican Prospect League in July 2011, receiving a reported bonus of $800,000. At age 17, he started his professional career with Rookie Level Dominican Summer League Red Sox in their 2012 season. In his professional debut, Margot earned Red Sox Minor League Latin Program Player of the Year honors, after batting a.285/.382/.423 with 38 stolen bases in just 68 games, gaining a spot on the DSL All-Star team. Regarded as a patient hitter, he walked more than he struck out in the DSL. Margot jumped up two levels to the Lowell Spinners in 2013, and played as the youngest regular in the Short-Season A New York–Penn League. Following his successful debut, Margot did manage to get a hit in 12 out of his first 15 games with Lowell, collecting a.254/.343/.307 line through July 24, when a hamstring injury laid him up. After a disabled list stint, he returned on August 16 showing glimpses of his potential with a.447/.475/.658 line over his first eight games back. He finished the year with a.270 average and 18 stolen bases in only 49 games. Margot played for the Low A Greenville Drive of the South Atlantic League in 2014. In his first 99 games at Greenville, he posted a.282/.362/.418 line with 10 home runs and 45 runs batted in, while leading the Drive with 105 hits and 61 runs scored, and the Red Sox organization with 39 stolen bases. As a result, he was promoted to High A Salem Red Sox of the Carolina League on August 15. In 2014, Margot hit.340/.356/.560 in just 18 games for Salem, combining for a.293/.356/.462 line with 12 homers and 59 RBI in 115 contests in the two stints. Besides, he led the Sox minors system with 42 stolen bases. It was just the latest part in what was a very solid season in the organization despite his youth. As such, he climbed from No. 11 to No. 4 in the MLB.com Top 20 Boston Red Sox Prospects list. In 2015, Margot improved his slash line up to.282/.321/.420 through 46 games with Salem, and earned a promotion to the Double-A Portland Sea Dogs in the midseason. His five triples were tied for third-most in the Carolina League, while his 20 steals in 25 attempts ranked fourth in the circuit at the time of his promotion. Soon after, MLB.com announced that he would be member of the World Team in the Futures Game prior to the Major League All-Star Game. Margot then posted a combined.271/.326/.419 batting line with 25 extra bases and 19 steals over 109 games played for the Sea Dogs. During the Sea Dogs annual Field of Dream Fan Appreciation Game at Hadlock Field, he hit for the cycle and drove in a season-high five runs as the Sea Dogs topped the New Britain Rock Cats, 10–5, becoming the first ever Portland player to hit a cycle at Hadlock Field. On November 13, 2015, the Red Sox traded Margot, Javier Guerra, Carlos Asuaje, and Logan Allen to the San Diego Padres for Craig Kimbrel. On November 19, 2015, the Padres added Margot to their 40-man roster to protect him from the Rule 5 draft. Margot began the 2016 season with the Triple-AEl Paso Chihuahuas, where he played in 124 games, including 117 starts in center field. He batted.304 with 6 home runs and a.777 OPS. The Padres promoted him to the major leagues on September 21, 2016.
In his September, 2016, call up, Margot played in 10 games, including seven starts in center field and one in right. Despite a knee injury that limited his playing time in spring training, Margot made the 2017Opening Day roster as the starting center fielder. Margot hit five extra-base hits in his first six games of the 2017 season, including two home runs in consecutive plate appearances against San Francisco Giants starter Matt Cain on April 8, and two doubles off of Giants starter Madison Bumgarner on April 9. Margot missed about a month of the season in May and June with a calf injury. Margot finished the 2017 season with a.263/.313/.409 batting line with 13 home runs in 126 games, including 121 starts in center field. He finished sixth in the NL Rookie of the Year voting. Margot was the Padres regular center fielder in 2018, starting 123 games there, and only missing 10 days on the disabled list with bruised ribs in April. His batting line on the season dropped to.245/.292/.384 with 8 home runs and 11 stolen bases. He was considered to be a plus defender in center field, without making many highlight plays. Margot began losing time in center field in 2019, making 98 starts there while Wil Myers picked up 58 of the center field starts. Margot effectively became part of a platoon with left-handed hitting corner outfielderJosh Naylor in the latter part of the season. Margot still played in a career-high 151 games on the season, often coming in as a pinch hitter or defensive replacement. Margot batted.234/.304/.387 on the year, with 12 home runs in 398 at-bats. He had 20 stolen bases in 24 attempts. On defense, Margot led the Padres with 11 outs above average, ranking fourth in the National League.
