At the start of the 2003–04 season, Morgenstern suffered a violent accident in Kuusamo, in which he was hit by a gust of wind just after takeoff, forcing him to flip over in mid-air and land hard on his back. He only sustained minor injuries, and managed to recover quickly to continue his success. He was second overall to Sigurd Pettersen during most of that season's Four Hills tournament, finally ending up in fourth place. He won his first team medal with a 3rd place at the Ski-Flying World Championships.