John Eliot (1604-1690) was known as the “apostle to the Indians” in both Old and New England during his lifetime. His goal of inculcating “civility” with religion among “praying Indians” is often noted as representing an agenda by New English missionaries for cultural assimilation. This dissertation argues that an appropriate understanding of Eliot’s motives and methodology in ministry to Native Americans obtains from a consideration of the Congregationalist and sacrament-centered spirituality he indicated in publications before and after King Philip’s War. Eliot’s mission was more shaped by ecclesiology than eschatology or the aim of cultural hegemony. Eliot intended “praying town” settlements in the Massachusetts Bay Colony to provide Native enquirers the kind of communitarian experience he believed essential for the establishment and maintenance of congregations comprised of genuine converts who could as members in good standing together practice the Lord’s Supper. Communal life with sacramental practice would be the ultimate way for them to experience Christ’s presence. This study extends previous scholarship by employing a theological perspective to explicate Eliot’s understanding of covenantal theology and the work of the Spirit of Christ through various “means of grace.” The project incorporates the perspectives of early American historians; Puritan scholars, especially historians of doctrine; literary critics; and recent studies of colonial encounter that posit cultural negotiation. This dissertation suggests that Eliot’s practices in mission reflect the meaning of Congregationalist Puritanism in colonial context. It adds to the emerging picture of a variegated transatlantic Puritanism and suggests that Eliot’s corpus should be considered in studies of Puritan pneumatology, Christology, sanctification, the sacraments, and religious declension. Eliot’s contribution as a contextual theologian becomes clear when his writings are examined alongside select documents from contemporary interlocutors such as Richard Baxter, Daniel Gookin, William Hubbard, Increase Mather, Mary Rowlandson, and Thomas Shepard. The study also suggests that Eliot’s later literary productions in English reflect his experience in cross-cultural ministry more than is currently recognized, especially his Lord’s Supper preparative, The Harmony of the Gospels, in the Holy History of the Humiliation and Sufferings of Jesus Christ (1678).