Cowen was traded to the Toronto Maple Leafs in February 2016, but never played for the franchise and retired in 2017, after a pre-season tryout with the Colorado Avalanche.

As the league's champions, the Chiefs subsequently earned a berth in the 2008 Memorial Cup, where they defeated the Kitchener Rangers by a score of 4-1.

[9] Compared by some scouts to Zdeno Chára[10] and Derian Hatcher,[11] Cowen was expected to challenge for a roster spot in Ottawa for the 2010–11 season.

He joined Ottawa's American Hockey League (AHL) affiliate, the Binghamton Senators after the Spokane Chiefs were ousted in the third round of the WHL playoffs.

[13] In 2011–12, Cowen made the Ottawa roster out of training camp and played regularly, being paired with veteran defenceman Sergei Gonchar.

By March 27, 2013, Cowen was able to practice with the Senators,[17] and he was finally able to return to the Ottawa lineup on April 16, 2013,[18] much sooner than initial estimate of six-to-eight months.

Cowen and the other players had originally intended to be at the marathon's finish line during the time at which bombs exploded, killing and injuring several spectators and runners.

Scratches for that night's game against the Boston Bruins, the players changed their plans at the last minute and elected to return to their hotel for a nap instead.

Cowen, Colin Greening, Milan Michálek, Tobias Lindberg and Ottawa's 2017 second-round draft pick were sent to Toronto in exchange for Maple Leafs captain Dion Phaneuf, Matt Frattin, Casey Bailey, Ryan Rupert and Cody Donaghey.

[34] After clearing waivers, Cowen filed a grievance against the Toronto Maple Leafs, claiming that since he was on the injury reserve, he could not be bought out of his contract.

[33][36] After sitting out the entirety of the 2016–17 season recuperating from injury, Cowen as a free agent agreed to professional tryout contract to attend the 2017 training camp of the Colorado Avalanche on August 30, 2017.

[41][42] On December 19, 2010, Cowen was named alternate captain for the 2011 Canadian junior national team to Ryan Ellis of the Windsor Spitfires, along with his fellow returnees, Brayden Schenn of the Brandon Wheat Kings and Calvin de Haan of the Oshawa Generals.