This essay describes a religious freedom controversy that developed between the world wars in the Belgian colony of the Congo, where Protestant missionaries complained that Catholic priests were abusing Congolese Protestants and that the Belgian government favored the Catholics. The history of this campaign demonstrates how humanitarian discourses of religious freedom—and with them competing configurations of church and state—took shape in colonial contexts. From the beginnings of the European scramble for Africa, Protestant and Catholic missionaries had helped formulate the “civilizing” mission and the humanitarian policies—against slavery, for free trade, and for religious freedom—that served to justify the European and U.S. empires of the time. Protestant missionaries in the Congo challenged the privileges granted to Catholic institutions by appealing to religious freedom guarantees in colonial and international law. In response, Belgian authorities and Catholic missionaries elaborated a church-state arrangement that limited “foreign” missions in the name of Belgian national unity. Both groups, however, rejected Native Congolese religious movements—which refused the authority of the colonial church(es) along with the colonial state—as “political” and so beyond the bounds of legitimate “religion.” Our analysis shows how competing configurations of church and state emerged dialogically in this colonial context and how alternative Congolese movements ultimately challenged Belgian colonial rule.