During the Indonesian War of Independence (1945-1949), the Dutch government deployed 220,000 soldiers in the Indonesian archipelago. Among them was a group of conservative Christian soldiers who refused vaccinations against smallpox for religious reasons. Initially this caused no problems, but the situation changed after the outbreak of a smallpox epidemic in Indonesia in 1948. The non-vaccinated soldiers could not return to the Netherlands due to international restrictions. Although compulsory vaccination was abolished in 1939, some soldiers were forced to accept vaccination. In the Netherlands, representatives of the Reformed Political Party (SGP) and the conservative churches accused the Army of illegal actions. The central question in the debate was the space for religious minorities and divergent views on vaccination in the Dutch Armed Forces. This article studies the process of negotiation between the Dutch Armed Forces and the political and ecclesiastical representatives of this conservative religious group. Finally, this article argues for more research into religious diversity in the Dutch Armed Forces.