History of the Puritans from 1649
From 1649 to 1660, Puritans in the Commonwealth of England were allied to the state power held by the military regime, headed by Lord Protector Oliver Cromwell until he died in 1658.
They broke into numerous sects, of which the Presbyterian group comprised most of the clergy, but was deficient in political power since Cromwell's sympathies were with the Independents.
With the creation of the Commonwealth of England in 1649, the government passed to the English Council of State, a group dominated by Oliver Cromwell, an advocate of religious liberty.
With no means to enforce uniformity in the church and with freedom of the press, these disputes were largely played out in pamphlet warfare throughout the decade.
In 1649, Richard Baxter, the minister of Kidderminster, Worcestershire and who served as chaplain to Colonel Edward Whalley's regiment, published a reply to Owen, entitled Aphorisms of Justification.
John Owen preached to the Long Parliament the day after the execution of Charles I, and then accompanied Oliver Cromwell to Ireland.
Two of his books – The Saints' Everlasting Rest (1650) and The Reformed Pastor (1656) – have been regarded by subsequent generations as Puritan classics.
Socinianism, an anti-trinitarian position, had made a few in-roads into England in the late sixteenth and early seventeenth centuries.
Adherents of this position had been brutally oppressed, with a number of high-profile executions, including that of Francis Kett in 1589, and Bartholomew Legate and Edward Wightman in 1612, after they in 1609 published a Latin version of the Racovian Catechism.
However, Cromwell, true to his principle of religious liberty, intervened to ensure that Biddle was not executed, but instead sent to exile on the Isles of Scilly in 1652.
Nevertheless, Charles II had hoped that the Book of Common Prayer could be reformed in a way that was acceptable to the majority of the Presbyterians, so that when religious uniformity was restored by law, the largest number of Puritans possible could be incorporated inside the Church of England.
At the April 1661 Savoy Conference, held at Gilbert Sheldon's chambers at Savoy Hospital, twelve bishops and twelve representatives of the Presbyterian party (Edward Reynolds, Anthony Tuckney, John Conant, William Spurstowe, John Wallis, Thomas Manton, Edmund Calamy, Richard Baxter, Arthur Jackson, Thomas Case, Samuel Clarke, and Matthew Newcomen) met to discuss Presbyterian proposals for reforming the Book of Common Prayer drawn up by Richard Baxter.
The Act of Uniformity prescribed that any minister who refused to conform to the Book of Common Prayer by St. Bartholomew's Day 1662 would be ejected from the Church of England.
Members of Cromwell's state church who chose to conform in 1662 were often labeled Latitudinarians by contemporaries - this group includes John Tillotson, Simon Patrick, Thomas Tenison, William Lloyd, Joseph Glanvill, and Edward Fowler.
Under the penal laws forbidding religious dissent (generally known to history as the Clarendon Code), many ministers were imprisoned in the latter half of the 1660s.
In March 1672, Charles issued his Royal Declaration of Indulgence, which suspended the penal laws against the dissenters and eased restrictions on the private practice of Catholicism.
In Europe, in the 17th and 18th centuries, a movement within Lutheranism parallel to puritan ideology (which was mostly of a Calvinist orientation) became a strong religious force known as pietism.
Virginia was a repository for more middle class and "royalist" oriented settlers, who were leaving England following their loss of power during the English Commonwealth.
Many migrants to New England who had looked for greater religious freedom found the Puritan theocracy to be repressive, examples being Roger Williams, Stephen Bachiler, Anne Hutchinson, and Mary Dyer.
