In the following season, Cooney continued to feature for Leinster in the league making a total of 13 appearances in the 2012–13 Pro12, scoring try against Scarlets on 23 February 2013. Nine of these appearances came as a replacement. In Europe, Cooney did not feature in the 2012–13 Heineken Cup as Leinster were knocked out in the pool stages. He did, however, come on as a replacement in three of the team's games in the 2012–13 European Challenge Cup, including the final against Stade Français, earning himself another European medal in the process.