Neuner competed at the Summer Biathlon World Championships for the first time in September 2009 when they were held in Oberhof. She only reluctantly agreed to interrupt training and participate in the summer event, which is contested on roller ski, however she went on to win gold in all three competitions (sprint, pursuit and mixed relay). Neuner missed the first World Cup of the 2009–10 season due to a cold in December 2009. She returned at the following races in Hochfilzen, but was still affected by her cold and finished outside the top 20. Her first podiums of the winter came in Pokljuka, finishing third in the sprint and second in the pursuit race. Thereby she secured her Olympic qualification within the German team.