He continued his success well into the 2003–04 season. He was second overall to Sigurd Pettersen during most of the 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.
In the 2006–07 season, he won the large hill team event at the Nordic World Ski Championships. Further, by reaching the 3rd place in the normal hill event he won his first individual medal at world championships. As in 2003, Morgenstern won the Ski jumping Grand Prix.
The season 2010–11 again started very successful by winning four of the first six competitions. Morgenstern further won the Four Hills Tournament for the first time in this season. In January 2011, he won his first ski flying event in Harrachov, and fixed his second victory of the ski jumping world cup with a 5th place at the ski flying competition on the Vikersundbakken on 13 February. At the 2011 FIS Nordic World Ski Championships in Oslo he won gold on the normal hill. It was his first gold medal in an individual event at world championships. In the following he further won gold medals in the team events (normal hill and large hill), both times together with Andreas Kofler, Martin Koch and Gregor Schlierenzauer, as well as the silver medal in the individual large-hill event.
As of 14 December 2013, Morgenstern has 23 World Cup victories, 3 Olympic gold medals, and 11 gold, 2 silver and 3 bronze medals at world championships.
On 10 January 2014 he suffered a serious head injury in training at Kulm for the ski jump worldcup.