Martin was a Florida State League All-Star catcher while with the Vero Beach Dodgers in 2004, playing 122 games and batting .250 with 15 home runs and 64 RBI. During the offseason, Martin played with the Scottsdale Scorpions of the Arizona Fall League. In 2005, he played in a career-high 129 games for the Double-A Jacksonville Suns and made the All-Star team, hitting .311 with 9 home runs and 61 RBI. Martin began the 2006 season with the Triple-A Las Vegas 51s, where he hit .297 in 23 games before his promotion.

Martin was promoted to the Dodgers on May 5, 2006, after a wrist injury to starting catcher Dioner Navarro. He got two hits, including a double, in the game. His first hit was against Chris Capuano. On May 7, he hit his first major league home run against Milwaukee Brewers pitcher Dave Bush. On June 6, 2006, Martin and Éric Gagné made baseball history by becoming the first French Canadian battery in the majors. Martin’s play was good enough that, on June 26, 2006, Navarro was traded to the Tampa Bay Devil Rays. On August 13, 2006, Martin hit his first career walk-off home run in a victory that completed a sweep of the rival San Francisco Giants. On September 18, 2006, Martin hit a solo home run off of Trevor Hoffman, the third of four consecutive home runs in the bottom of the 9th inning to tie the San Diego Padres. It was the first time four home runs had been hit in a row since the 1964 Minnesota Twins.

On April 21, 2007, Martin hit a walk-off grand slam against Pittsburgh Pirates pitcher Shawn Chacón in the bottom of the 10th inning. This was the first grand slam of his career.

In May 2007, Martin broke the Dodgers’ franchise record for single-season steals by a catcher (12) set by John Roseboro in 1962. On July 1 it was announced that Martin finished in first place in All-Star Game voting, leading Paul Lo Duca by 296,948 votes. He became the first ever Canadian born catcher to start the All-Star Game.

On May 2, 2008, Martin started his first game at third base since reaching the Majors, allowing veteran backup Gary Bennett to spell Martin behind the plate. Martin made his second all-star game during the 2008 season. He caught 10 innings of a 15 inning game in which the American League won 4 to 3. Martin’s 10 innings caught are tied for fourth place all time among all star catchers in a single game.

On January 20, 2009, Martin signed a one-year, $3.9 million contract to avoid salary arbitration. The deal was the largest ever awarded to a catcher in his first year of arbitration. He played for the Canadian team during the 2009 World Baseball Classic and then rejoined the Dodgers. He slumped offensively in 2009, hitting only .250 with 7 home runs in 143 games, the weakest totals in his four-year career.

In an effort to quit the use of chewing tobacco in 2009, Martin began wearing a custom-fitted mouthpiece during the WBC and Spring training.

In 2010, Martin continued to regress as he hit .248 with 5 home runs and 26 RBI in 97 games. In August, Martin suffered a torn labrum in his right hip when he was trying to avoid a tag at home plate in a game against the Padres. The injury kept him sidelined for the rest of the season.

Along with Robinson Canó and Curtis Granderson, Martin was one of the Yankees’ three batters who hit an MLB record three grand slams in a single game in a 22–9 rout of the Oakland Athletics at Yankee Stadium on August 25, 2011.

On November 29, 2012, Ken Rosenthal reported that the Pittsburgh Pirates had signed Martin for two years and $17 million. The deal became official on November 30. On June 4, 2013, Martin made his first start and appearance at right field. On June 8, 2013, Martin hit his 100th career home run.

In the NL Wild Card Game on October 1, 2013, Martin hit a pair of solo home runs as the Pirates defeated the Cincinnati Reds 6-2. The first was an infamous home run off Reds starter Johnny Cueto. Cueto, having his name chanted by 40,000 Pirates fans, dropped the ball while on the mound. His next pitch, a fastball over the heart of the plate, was crushed into the left-field stands by Martin. This home run gave the Pirates the momentum to win the game, their first postseason victory in 21 years.

During a game against the Milwaukee Brewers on April 20, 2014, Martin was involved in a brawl which was started when Carlos Gómez hit a triple off Gerrit Cole after which Martin was suspended 2 games by the MLB on April 22, 2014 for his role in the brawl.

On November 18, 2014, the Toronto Blue Jays announced that they had signed Martin to a five-year, $82 million contract. Early in spring training, manager John Gibbons told reporters that Martin would be R.A. Dickey’s catcher during practice and in preseason games, to give him the opportunity to practice catching Dickey’s knuckleball. Martin received a standing ovation from the fans at Olympic Stadium on April 3, as the Blue Jays played their final two spring training games in Montreal for the second consecutive year. On April 19, 2015, Martin caught Jeff Francis in his debut for the Blue Jays, and in doing so formed the first all-Canadian battery in franchise history. On June 2, Martin stole home off the back end of a double steal, and became the first Blue Jay to steal home since Brett Lawrie did so in 2012. Martin established a new career-high in home runs on September 26, hitting his 22nd of the season to aid the Blue Jays to a 10–8 win over the Tampa Bay Rays. He ended the 2015 regular season with a .240 batting average, 23 home runs, and 77 RBI in 129 games. He led the major leagues in passed balls, with 19. Martin was announced as a finalist for the catcher Gold Glove award, along with Salvador Pérez and Jason Castro.

Martin appeared in 137 games for the Blue Jays in 2016, and hit .231 with 20 home runs and 74 RBI. He struggled in the postseason, recording only three hits in 33 at-bats.

On December 5, 2016, Martin committed to play shortstop for Team Canada at the 2017 World Baseball Classic. However, Martin was left off Team Canada’s WBC roster on February 8, 2017, due to insurance complications relating to his offseason minor knee surgery.

On April 29, 2017, Martin became the 15th catcher to record 10,000 career putouts at the position.

On June 20, 2018, Martin became the 11th catcher to make 11,000 career putouts at the position. Martin endured his worst offensive season of his career, hitting .194 with 10 home runs and 25 RBIs. In the final game of the 2018 season, Martin managed the Blue Jays, the team wound up losing in his managerial debut.

On January 11, 2019, the Blue Jays traded Martin to the Dodgers for prospects Ronny Brito and Andrew Sopko. The Blue Jays also sent $16.4 million to offset most of Martin’s $20 million salary. Martin spent the 2019 season as the Dodgers backup catcher, first behind Austin Barnes and then Will Smith.

On March 30, 2019, Martin pitched the top of the ninth inning against the Arizona Diamondbacks. He made ten pitches and retired three straight batters and became the first primary position player to do so since left fielder Willie Smith got the final out of a Detroit Tigers win over the Washington Senators on September 23, 1963. Martin was the first full-time position player to work a 1-2-3 ninth in a team win since at least 1925. On August 28, 2019, Martin became the first position player to pitch in a shutout victory since October 3, 1917 when George Kelly of the New York Giants did so. Martin played in 83 games for the Dodgers in 2019, hitting .220 with six homers and 20 RBI. Besides catcher, he also played in seven games at third base and pitched four scoreless innings in four relief appearances for the Dodgers during the season, allowing only two hits.