Preventable chronic diseases account for the greatest burden in the German health system and statutory health insurance (SHI) funds play a crucial role in implementing and financing prevention strategies. On the contrary, the morbidity-based scheme to distribute financial resources from the Central Reallocation Pool among the different sickness funds may counteract efforts of effective prevention from an economic perspective. We assessed financial impacts of prevention from a sickness funds perspective in a retrospective controlled study. Claims data of 6,247,275 persons were analyzed and outcomes between two propensity-matched groups (n = 852,048) of prevention users and non-users were compared in a 4-year follow-up. Using a difference-in-differences approach, we analyzed healthcare expenditures, the development of morbidity, financial transfers from the Central Reallocation Pool, and contribution margins. The group of prevention users develops less morbidity (incidences and disease aggravations) compared to the control group. Healthcare expenditures increase in both groups within 4 years, whereas the increase is lower for prevention users compared to non-users (€568.04 vs. €640.60, p < 0.0001). Taking morbidity-based financial transfers into account, the decrease in contribution margins is stronger for prevention users (- €188.44 vs. - €138.73, p < 0.0001). This study demonstrates an economic disincentive from a sickness funds' perspective. In the semi-competitive SHI market, sickness funds will be discouraged from effective prevention strategies if investments are not worth it financially. Their efforts and knowledge are, however, crucial for joint action to foster prevention over cure in the health system.