The Seattle Mariners selected Saunders in the 11th round of the 2004 MLB draft. He then spent the 2005 season with the Everett AquaSox of the Short Season-A Northwest League, hitting .270 with seven home runs and 39 runs batted in (RBI). In 2006, he was promoted to the Wisconsin Timber Rattlers of the Class-A Midwest League, hitting .239 with four home runs and 39 RBI. Despite struggling in 2006, for 2007 he was promoted to the High Desert Mavericks of the Advanced-A California League, where he excelled, hitting .299 with 14 home runs and 77 RBI, before he was called up to the West Tenn Diamond Jaxx of the Double-A Southern League, where he finished off the season hitting .288 with one home run and seven RBI in 15 games. Saunders started the 2008 season once again in West Tenn, where he hit .290 with eight home runs and 30 RBI in 67 games before being promoted to the Tacoma Rainiers of the Triple-A Pacific Coast League on June 17.

After beginning the 2009 season with the Rainiers where he hit .313 with 13 home runs and 32 RBI in 243 at-bats, Saunders was promoted from Tacoma on July 25, 2009, when the Mariners designated Wladimir Balentien for assignment. He made his MLB debut that day in a game against the Cleveland Indians at Safeco Field, where he went hitless against Jeremy Sowers in the Mariners 10–3 loss. His first MLB hit was a single off of Cliff Lee on July 26, 2009.

On May 6, 2010, Saunders was recalled from Tacoma after the Mariners put Milton Bradley on the restricted list. Three days later, he hit his first MLB home run off Angels pitcher Ervin Santana. He finished the 2010 season with a .211 batting average, 10 home runs, and 33 RBI. Saunders played only 58 games for the Mariners in 2011, and batted .149 with just two home runs and eight RBI.

In 2012, Saunders played a career-high 139 games and greatly improved upon his 2011 campaign. He hit .247 with 19 home runs and 57 RBI. He played in 132 games the following season. Saunders finished 2013 with a .236 batting average, 12 home runs, and 46 RBI. In 2014, Saunders battled a number of injuries that limited him to 78 games, but finished with a career-high .273 average with 8 home runs and 34 RBI.

At the end of the 2014 season, Jack Zduriencik, the general manager of the Mariners, publicly criticized Saunders’ work ethic, which Saunders challenged. On December 3, 2014, the Mariners traded Saunders to the Toronto Blue Jays in exchange for pitcher J. A. Happ. Saunders agreed to a one-year, $2.875 million contract on January 16, 2015, to avoid salary arbitration.

On January 15, 2016, Saunders and the Blue Jays avoided salary arbitration by agreeing to a one-year, $2.9 million contract. In a 13–3 win over the Baltimore Orioles on June 17, Saunders hit three home runs for the first time in his career, and joined Joey Votto, Justin Morneau, and Larry Walker as the only Canadian players to hit three in a game and becoming the first to do it for a Canadian team. He also had eight RBI in the game, which established another career-high. Saunders was named as one of five candidates for the All-Star Game Final Vote campaign on July 5. He was announced as the Final Vote winner on July 8. After the All-Star break, Saunders struggled to a .178 batting average, eight home runs, and 15 RBI. Despite the poor second half of his season, Saunders still established several career-highs in 2016. He ended the campaign with a .253 batting average, 24 home runs, and 57 RBI in 140 games played. He appeared in eight postseason games for the Blue Jays, and hit .381 with one home run and RBI.

On January 16, 2017, Saunders agreed to a one-year, $8 million contract with the Philadelphia Phillies that also includes a $9 million club option for the 2018 season. The contract became official on January 19. He struggled to a .205 average with six home runs for the last place Phillies during the first three months of the season. On June 20, Saunders was designated for assignment by the Phillies. He was released three days later.

On June 28, 2017, Saunders signed a minor league contract with the Toronto Blue Jays. On August 31, Blue Jays’ manager John Gibbons announced that Saunders would be called up on September 1.

Saunders signed a minor league contract with the Pittsburgh Pirates on February 21, 2018. After Pittsburgh acquired Corey Dickerson the following day, Saunders requested his release from the team. On February 23, he signed a minor league contract with the Kansas City Royals. The Royals released Saunders on March 24, and he signed a minor league contract with the Baltimore Orioles on April 2. On May 15, Saunders asked for and was granted his release by the Orioles.. On May 21, 2018, Saunders signed a minor league deal with the Chicago White Sox. He was released on June 21, 2018.

On December 30, 2018, Saunders signed a minor league deal with the Colorado Rockies. He was released on March 17, 2019.

On January 9, 2019, he was selected Canada at the 2019 Pan American Games Qualifier.

On October 8, 2019, he was selected at the 2019 WBSC Premier12.

On October 25, 2019, Saunders announced that he would retire following the 2019 WBSC Premier12, and become a minor league coach in the Atlanta Braves organization in 2020.