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The lead up to the Civil War of the 1640s is woven with issues relating to politics, economic and social change, and religion. The rise in literacy following the translation of the Bible into the vernacular language helped the spread of new ideas in England, and some of these in turn spread into the border areas of Wales.

Bristol was a very influential centre of early Nonconformity, and it is no coincidence that the first Nonconformist chapel in Wales was founded by Congregationalists in Llanvaches, Monmouthshire, in 1639, near the border with England.

Dissatisfaction with the reign of Charles I found a home within the emerging Puritan movement, which ultimately led to regime change and the previously unthinkable - the legal execution of the King of England in 1649 followed by the establishment of a Protestant Republic led by .

One of the first acts of the Puritan regime was the passing in 1650 of the . During the war Wales had been almost entirely Royalist, confirming the puritan view of Wales being a 'dark corner', and here the Act was applied to root out dissident clergymen. Radnorshire born Vavasor Powell came to prominence as a particularly enthusiastic, and feared, enforcer of this new law.

However, the Act also created new schools which taught children to read and write, although their work was hampered by the insistence on using English as the sole medium of instruction. Wales was still largely monoglot Welsh speaking at the time.

Within a couple of years of Cromwell's death in 1658 the monarchy returned to Britain. The Restoration was accompanied by a series of legal measures against Nonconformist sects which became known as the .

In Wales the Quakers in Montgomeryshire became the targets of persecution. One of the most famous cases involved the Lloyds of Dolobran, a prominent and much respected old family. Members were thrown into jail as a consequence of their beliefs. Some Quakers responded by moving to the American colonies in search of religious tolerance, and became prominent members of the in America.

Another Protestant sect which had members fleeing to America at this time were the Baptists. John Miles was the founder of the first Baptist congregation at , in 1649. During the 1650s he built on this success, establishing chapels elsewhere across south Wales as well as being to official positions, yet the Restoration brought this progress to an abrupt end. The chapels withered away and John Miles was to end his days in a town he founded in Rhode Island called Swansey.

The end of the decade saw the of 1689 when the Protestant monarchs William and Mary took the throne, and the Bill of Rights Act, which ushered in an era of religious toleration.