Particularly in the years after 1630, Puritans left for New England, supporting the founding of the Massachusetts Bay Colony and other settlements. The large-scale Puritan emigration to New England ceased by 1641, with around 21,000 having moved across the Atlantic. This English-speaking population in America did not all consist of original colonists, since many returned to England shortly after arriving on the continent, but produced more than 16 million descendants. This so-called "Great Migration" is not so-named because of sheer numbers, which were much less than the number of English citizens who emigrated to Virginia and the Caribbean during this time.

The Plymouth Colony Puritans of New England disapproved of Christmas celebrations, as did some other Protestant churches of the time. Celebration was outlawed in Boston from 1659. The ban was revoked in 1681 by the English-appointed governor Sir Edmund Andros, who also revoked a Puritan ban on festivities on Saturday nights. Nevertheless, it was not until the mid-19th century that celebrating Christmas became fashionable in the Boston region.

The Puritans of the Massachusetts Bay Colony were the most active of the New England persecutors of Quakers, and the persecuting spirit was shared by the Plymouth Colony and the colonies along the Connecticut river. In 1660, one of the most notable victims of the religious intolerance was English Quaker Mary Dyer, who was hanged in Boston for repeatedly defying a Puritan law banning Quakers from the colony. She was one of the four executed Quakers known as the Boston martyrs. In 1661, King Charles II explicitly forbade Massachusetts from executing anyone for professing Quakerism.

Early New England laws banning the sale of alcohol to Native Americans were criticized because it was "not fit to deprive Indians of any lawful comfort aloweth to all men by the use of wine." Laws banned the practice of individuals toasting each other, with the explanation that it led to wasting God's gift of beer and wine, as well as being carnal. Bounds were not set on enjoying sexuality within the bounds of marriage, as a gift from God. In fact, spouses were disciplined if they did not perform their sexual marital duties, in accordance with 1 Corinthians 7 and other biblical passages. While it would seem that women would be most commonly persecuted for such accusations, men were equally (if not more so) expected to fulfill marital responsibilities.