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.
In 1633, Plymouth Governor John Bradford commented that Williams had begun to express and practice "strang opinions," eventually resulting in the preacher leaving the church. His complaint was that when Plymouth citizens returned to England, they would participate in Anglican services, thereby contaminating the Plymouth church upon their return. Williams returned to Salem where the people appointed him an assistant to the minister, and he immediately set out to purify the Salem church.
Winthrop and other colonial leaders began to question him about a statement that he made in Plymouth, which attested that the colonists had no right to the land they occupied. Williams stated that the king governed by a "solemn public lie" and had no right to grant land to the colony. The General Court promptly ordered Williams to appear at its next meeting to be censured. Winthrop tried to minimize the confrontation and wrote to Williams, pointing out ways for him to qualify his statements to the court. Williams behaved satisfactorily for the court, and nothing more was said of the incident.
However, in November 1634, six months after Winthrop had been removed as governor, word reached the court that Williams had begun teaching his beliefs again. He was telling settlers that the charter needed to be rewritten or the entire colony would have to be dissolved to "purify" it. When the General Court recalled Williams, the ministers of the area asked instead to counsel the transgressor privately–thus preventing Williams from sending a drafted letter to the king accusing him of lying. Again and again over the next year Williams was resummoned to appear in front of the court, each time after having violated the Puritans' mores. The punishment, though, had little effect on his congregation, and in the spring of 1635, the Salem church appointed him full pastor.
The General Court and other ministers reacted strongly. While the churches were unable to act against Salem to prevent Williams's teachings, the civil government had no such qualms. Salem had asked for more land on a nearby peninsula, and the General Court announced that the town could only get the land if it removed Williams from his position–a move which angered Salem residents. They appealed to other area churches for help, but their appeals fell on deaf ears. As the court did battle against Salem, the entire colony might have collapsed if Williams not been confined to his house because of an illness; he could only communicate by letters and thus his charm was lost on both Salem and the court. He asked the people of Salem to renounce all other churches and declare themselves the one "true" church–a dangerous and isolating move. Salem balked.
In a final confrontation, the General Court called Williams to appear in October, 1635 where it ordered him to leave the colony within six weeks. It later extended the deadline until the following spring, but in January 1636 Williams left Massachusetts Bay with a band of followers and headed for Narragansett Bay in nearby Rhode Island.
For now, the Puritan church and their set of beliefs were safe. Winthrop had deftly managed the biggest crisis facing the new colony and once again saved it from possible ruin.