He played in Major League Baseball (MLB) for the Minnesota Twins, Boston Red Sox, and Oakland Athletics.

[1] Bonser was selected out of high school by the San Francisco Giants in the first round (21st overall) of the 2000 Major League Baseball draft.

[5] From 2002 through 2003, Bonser progressed steadily through the Giants' system, reaching the Triple-A level at the end of the 2003 season with the Fresno Grizzlies.

[3] On November 14, 2003, Bonser was traded to the Minnesota Twins organization, along with pitchers Joe Nathan and Francisco Liriano, for catcher A. J. Pierzynski, and cash.

[6] Bonser was assigned to Double-A New Britain for 2004, and was promoted to the Triple-A Rochester Red Wings for a spot start at the end of the season.

[3] As Bonser continued to pitch in the minors without any further breakout seasons, his status as an elite prospect faded, but after a fast start at Rochester in 2006 in which he posted an earned run average of 2.01, he was promoted to the majors.

[13] By August 12, Liriano had been placed on the disabled list, and Bonser was back in Minneapolis to face the Toronto Blue Jays.

Although he lost the game, allowing seven hits and three runs over 5+2⁄3 innings, Twins manager Ron Gardenhire decided to keep him in the starting rotation.

He had struggled with stamina and pitching late into ball games during the 2007 season, so the Twins encouraged him to lose weight, which he accomplished by a healthier diet, combined with more intense exercise.

[21] However, Bonser's weight loss did not help his starting pitching performances through May 31, as he compiled a mark of 2–6 with a 6.16 earned run average, and was demoted to the bullpen to make room for Scott Baker.

[24] On February 25, 2009, Bonser underwent surgery to repair tears in his labrum and rotator cuff, and missed the entire 2009 season.

After posting a 5.87 earned run average at Triple-A Fresno, the Giants released Bonser from his minor league contract on June 27.

[3] He finished the season in Taiwan with the Uni-President 7-Eleven Lions of the Chinese Professional Baseball League, going 1–0 with a 1.76 ERA in 11 relief appearances.

[3] Bonser joined the Bridgeport Bluefish of the Atlantic League of Professional Baseball Clubs where he appeared in 12 games, pitched 16.2 innings, and struck out 15 batters while going 2–0 with a 2.16 earned run average.