During the closing games of the 2007–08 football season in May 2008, Grønkjær sustained a knee injury. The injury became infected by staphylococcus, and required three bouts of surgery. He did not recover until halfway through the 2008–09 football season, when he rejoined the Copenhagen team for a friendly match against Swedish team Malmö FF in January 2009. By the end of that season he had again earned a place in the starting line up, as Grønkjær helped Copenhagen win the Double of both 2008–09 Danish Superliga championship and the 2008–09 Danish Cup trophy. Grønkjær played the highest number of games in his Copenhagen career during the 2009–10 football season, as he helped the club win the 2009–10 Danish Superliga championship.
