One of the most lasting contributions of Winthrop to the Massachusetts Bay Colony was his heavy reliance on religion. While still aboard the Arbella, Winthrop and the other founders laid down their religious hopes for the new colony in a document called the "Model of Christian Charity." In it he laid out how the Puritans would remain pure so that God would continue to bless the colonists while they awaited their chance to return and save England from eternal hellfire. He repudiated the Church of England, its hierarchy, and its ceremonies. However, they walked a fine line since the king would revoke the charter if he discovered they had disavowed the Anglican faith.
In order to preserve the sanctity of the new colony, discipline became one of the biggest issues among the religious group, much of which was conducted on the family level. In fact, family discipline became so important that the colony prohibited anyone from living alone, and single men and women were required to move in with other families. Issues that were too large for a family to control–those that affected the whole community–came in front of the General Court for even the God-fearing colony suffered from the devil's influence. Winthrop carefully recorded the transgressions of his fellow colonists in his journal. Retribution was always quick and harsh. For instance, in one of the more bizarre cases, George Spencer was executed after one of his pigs sired a piglet with human resemblances. The "saints" of the new colony found it easy to pass harsh judgments against sinners among them, since they knew that God's judgment would be just as quick. If church and God had been a part of everyday life back in England, the settlers intentionally made it their entire lives in the New World.
The first church in Massachusetts, a congregational church in Salem, had been founded the year before Winthrop's party arrived. By 1635 there were more than a dozen churches scattered around the area. The process to join a church was rigorous, as members had to apply to the minister and explain their conversion. However, Winthrop believed that most people who made the journey to the New World had already proved their dedication to God by seeking out a pure environment.
The Puritan faith believed strongly in the strength of the individual, and it shunned the hierarchies of more established churches like the Church of England and the Roman Catholic Church. One problem with this belief, however, was the Puritan church had no specific orthodoxy or control over what individual churches taught–an oversight that caused several major crises for the new colony.
In 1631, George Phillips, the pastor of the Watertown church, began teaching his congregation that both the Church of England and the Catholic Church were "true" churches–the opposite of what the Puritan faith held, which was that both were too corrupt for God. Winthrop journeyed to Watertown to debate the pastor in front of the congregation. At the end of the night, all but three members of the church admitted Phillips's teachings and their beliefs had been in error.
A more serious crisis involved a well-spoken and charming preacher named Roger Williams. The problem with forming a colony to attract religious separatists was that they often were not afraid to take stands against the government and the established positions of the church, even an separatist church like the Puritan church itself. Williams had been involved in the Massachusetts Bay project from its earliest days, even attending the first meeting in 1629. When Williams arrived abroad the Lyon in the middle of the first winter, Winthrop hailed the arrival of the "godly minister." Then Williams was invited to become pastor of the Boston church but refused, believing that the Boston church was too impure for him since not everyone in the church condemned the Anglican Church. Winthrop sharply criticized Williams, calling his opinions wrong and hinting that he would use his authority to keep the church from negotiating to get Williams. Williams left for Salem but not before threatening that Winthrop's civil authority could not intervene in church matters. The Salem church, run by John Endecott, welcomed him with open arms until, Winthrop wrote to Endecott "marveling" that the town would accept such a dangerous minister. Williams finally settled in Plymouth, outside of Winthrop's sphere of influence. He would not be content there for long.