In the 2015–16 season, Cowen struggled to solidify himself within the Ottawa lineup, occasionally seeing himself a healthy scratch. On February 9, 2016, Cowen was included in a blockbuster, nine-player trade with the Toronto Maple Leafs. Cowen, Colin Greening, Milan Michalek, 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. On February 26, 2016, Cowen was placed on waivers by the Maple Leafs and then assigned to their AHL affiliate, the Toronto Marlies. Cowen was then sent home by Toronto to await a buyout and given the freedom to contact other teams about a new contract for the 2016–17 season; buying-out Cowen's contract would provide the Leafs with a $650,000 salary cap credit for the 2016–17 season.