In standard postcolonial political polemics in Uganda, colonial Anglican and Catholic churches have been castigated for fomenting and exacerbating Uganda's political divisions. These polemics overlook the growing ecumenical ties between Catholic and Anglican leaders that began in the 1950s and continued well into the 1980s. In particular, the shared experience of political oppression forged solidarity between erstwhile Catholic and Anglican rivals, especially during the Idi Amin dictatorship of 1971–1979 and the brutal civil war of 1979–1986. Drawing on an array of archival, oral, and secondary sources, this article offers a synthesis of Ugandan Christian leaders’ political engagement during the quarter-century following independence in 1962. I argue that church leaders in the 1960s embraced a politically quiescent, “social development” approach best embodied in the ecumenical Uganda Joint Christian Council. In the early 1970s, Anglican and Catholic leaders slowly withdrew from active collaboration with Amin's regime, embracing an approach I term “prudent recalcitrance,” entailing shifting stances of official silence, private lobbying, and carefully crafted written critiques. Finally, during the political unrest and civil war of the early 1980s, church leaders adopted a posture of “prophetic presence,” standing for and with the people in opposition to Milton Obote's increasingly violent state.