Through the later seventeenth century, Protestant missions in English America were surrounded by controversy. Missionaries working with Amerindians and enslaved Africans were accused of threatening the stability of overseas dominions. Crown officials were alleged to have impeded evangelism, and colluded in a culture of colonial godlessness. In modern scholarship, these conflicts have been located within a context of long-term tension between “religion” and “empire.” This article suggests that they were rooted in the transatlantic divisions within English Protestantism, and in political conditions peculiar to the 1660 Restoration. Colonial missions developed competitively and acrimoniously, when the Church of England vied against Protestant rivals in America, and when ecclesiastical policy in England remained unsettled. Battles for converts between Anglicans, Quakers, and Congregationalists stirred disputes over the management of England’s multi-confessional dominions. Simultaneously, they raised questions over how a colonizing kingdom could export the reformed religion, when its own confessional environment was severely divided.