As Black church leaders decried the arrival of Jim Crow segregation, many also celebrated the racial independence of their churches. They touted advancements such as women's ordination as examples of what Black churches could do when freed from white control. Other Black ministers defended remaining in majority-white denominations as a way to abolish the color line. This article argues that scholars miss much about Black religious history if we assume that Black churches’ resistance to racial subjugation started with a settled and uncontested racial autonomy. On the contrary, Black churches throughout the nineteenth century kept open a lively forum about the virtues and vices of such autonomy. Interracial cooperation often undermined Black autonomy, and Black Christians debated which better countered racial caste. To track the heated debates over racial independence and interracial cooperation within and between Black churches, this article analyzes Black newspapers, sermons, church minutes, and letters, mostly among Black Methodists but also among Black Baptists and Presbyterians throughout the late nineteenth century. It focuses on particular debates surrounding women's ordination, attempts to unite Methodists, and conflicts over Baptist education.