Neuner's preparation for the 2008–09 season was affected by several illnesses. In the summer, she battled an intestinal fungus which forced her to pause training for seven weeks; she later attributed it to pressure of public expectations. In October 2008, she contracted influenza and in November, a bacterial infection caused her to miss two weeks of training. Subsequently, her ski speed saw a substantial drop at the start of the season. In the first four World Cups, Neuner only achieved two individual podiums; atypically courtesy of good shooting performances, not her skiing.