In 2006, Clemens played with the Class A Lexington Legends of the South Atlantic League, where he batted .229 with 5 home runs and 39 RBIs in 91 games.

[8] In the 2006 Hawaiian Winter League, playing for North Shore Honu, Clemens batted .196 with one home run and nine RBIs in 32 games.

In June 2009, he returned to play with the Lancaster JetHawks of the Class A-Advanced California League in the roles of a catcher and designated hitter.

In 2011, Clemens was with the Houston Astros' Triple-A affiliate, the Oklahoma City RedHawks of the Pacific Coast League, as their first baseman.

Clemens started playing at the Puerto Rico Baseball League with the Mayagüez Indians as a first baseman in the fall of 2011.

There were rumors his father persuaded him to leave the island because of the kidnapping of Washington Nationals catcher Wilson Ramos in Venezuela the day before.

During the 2012 season, he played for the Blue Jays' Double-A affiliate, the New Hampshire Fisher Cats of the Eastern League, and their Class A-Advanced team, the Dunedin Blue Jays of the Florida State League as a catcher, first baseman, third baseman, outfielder, and designated hitter.

[11] Clemens played one game for the Sugar Land Skeeters of the independent Atlantic League of Professional Baseball in 2012, then returned to the team for the 2013 and 2014 seasons.