Established in 1662, the New England Company introduced the first crown-sponsored initiative for propagating the gospel among the native populations bordering English America. Under the leadership of Robert Boyle, its work influenced royal policy, but awakened contention over the practice of Atlantic colonization and, simultaneously, the making of the Restoration Church. This article examines the reception of the Company in England, showing how its architects sought to link the plantation process to the advancement of a global Protestant mission. The ambition drew Company leaders into debates over the reshaping of church institutions on both sides of the Atlantic. In England, the mission became a vehicle for the promotion of Protestant ‘comprehension’, as a bid to unite the different streams of the reformed religion, and widen the fold of the established church. However, the Company was frustrated by the confessional antagonisms that entered into domestic politics. Divisions between congregations thwarted missionary collaboration, and stirred doubts in England and America over the relationship between colonization and the ‘Protestant interest’. The article will identify the conflicts within the Restoration Church as a formative factor behind competing ideas of overseas expansion, and a substantial obstacle to the emergence of the Protestant mission as part of the colonizing strategies of the English Crown.