Clowe played 11 games for the Sharks in 2007–08, then went on injured reserve on October 28, 2007, due to torn knee ligaments.

He returned to the lineup on March 30, 2008, in time for the 2008 playoffs, during which he recorded 9 points in 13 games, which was second-best on the team behind only Joe Thornton.

On April 5, 2012, Clowe reached out from the bench with his stick to illegally interfere with Los Angeles Kings centreman Jarret Stoll.

Clowe was assessed a minor penalty for roughing and a game misconduct for leaving the bench on an illegal line change to start a fight.

)[7] On July 5, 2013, as an unrestricted free agent, Clowe signed a five-year, $24.25 million contract with the New Jersey Devils.

On September 12, 2015, Clowe retired from the NHL after team doctors refused to clear him to return to the ice following a concussion initially sustained in a November 6, 2014, game against the St. Louis Blues.