According to John Cotton, the theology of religious establishment in the magisterial Protestant tradition upheld the demands of uniformity without compromising the sacredness of the human conscience. This paper provides an analysis of John Cotton’s theology of religious establishment and how the politics of conformity coalesced with Cotton’s contention that the human conscience belonged to God and God alone. As such, the contest of religious liberty in the early modern period cannot simply be reduced to a debate between the conscience’s persecutors vs. the conscience’s liberators. On the contrary, the theology and politics of religious establishment emerged from a complex doctrinal system that complicates simplistic narratives regarding the debates and controversies over freedom of conscience. To prove this thesis, this paper will situate Cotton within his historical context, showing lines of connection to his theological forbears, especially William Perkins. Cotton’s polemics against Roger Williams, as well as his letters during his time in the Massachusetts Bay Colony will provide the primary literary evidence to prove the main assertions of this paper. Finally, this paper will briefly chronicle how Cotton’s theology of conscience persisted in Massachusetts, framing the colony’s justification in its handling of policies against Baptists and Quakers.