The works of John Edwards had done much to divide Presbyterians from the Independents in a way which only benefitted the Royalists, who revelled in the dissension among their opponents.

By the end of 1646 the First Civil War had come to an end. The battle of Stow on the Wold was the last defeat of the last Royalist army.

Despite a largely puritan population, about 50 well to do Suffolk families remained pro-royalist, notably the Jermyn family at Rushbrooke. Sir William Hervey of Ickworth even raised a regiment for Charles I in the civil war.

In the years from 1643 to 1646 about 129 Anglican clergy from Suffolk's total of 517 were hauled up before Committees and accused of being scandalous or malignant. They were evicted from their livings and four fifths of their property was "sequestered" or confiscated. Virtually anybody who had accepted the directions of Bishop Wren in the late 1830's was put on trial. Even being an inadequate preacher brought penalties.

Public disquiet about Matthew Hopkins and his witch hunts were to force Hopkins to abandon them by 1647. Although he is sometimes said to have been executed himself, he probably died of Tuberculosis.

George Fox, a Leicestershire puritan from a weaving family began to preach about his "great experience" of God and his speeches sometimes caused a shaking or quaking in his audience. Thus began the Quaker movement or Religious Society of Friends, who would soon become significant in local history.

Some 150 Apprentices gathered on Christmas Day and were intent on enforcing shop closures and threatened to kill any traders that opened their doors. They armed themselves with heavy clubs studded with nails. There was bloodshed reported in the Horse Market and at least two people were seriously injured. John Lansetter's shop in Cook Row was particularly targeted because of his well known position as an Independent and a pamphleteer. Extreme Puritans viewed this riot as a "horrid plot and bloody conspiracy," as shown in the attached picture of a pamphlet issued at the time.

Perhaps the oddest thing about these riots is that the disputes were between what we would see as different degrees of Puritanism. The "established" version of Puritanism were the Presbyterians, while the rest were known as "Independents". One such Independent was John Lanseter or Lanceter of Cook Row in Bury St Edmunds. Lanseter was against Christmas as a pagan and Popish invention, and so he felt that he should continue to open his shop and trade as normal on Christmas Day. Royalist supporters, known as 'malignants' to the pamphlet author were happy to side with Prebyterians against Lanseter's stand and provoke a riot which threatened Lanseter's life and property.

At Stowmarket there was a "tumultuous assembly", and drums were beaten, but the authorities soon dispersed them.

At Bury St Edmunds a defiant crowd gathered on 12th May to protest about the Puritan restrictions on the old revels of May. Just as they were erecting a Maypole for the traditional , but long banned Maypole dancing, a troop of Lord Fairfax's cavalry rode into town. The rowdy crowd shouted out for "God and King Charles", and chased the no doubt bewildered cavalry out of town. Things escalated when the crowd decided to seize control of the powder magazine and put the town into a state of defence.

By now the crowd was said to number 600, with a further 100 mounted on horseback. Although this disturbance was called a Royalist rebellion, and indeed it was so, it was not a serious military threat. Parliament regained the town in two days on 15th May. The rioters are said to have "yielded to mercy". There does not seem to have been any organised leadership, and seems to have been a protest by working people. Colchester was besieged by the Parliamentary army on 13th June, and finally surrendered after a two month siege. The parliament's New Model Army had Lord Thomas Fairfax as its Commander in Chief, and he led the siege. This was one of the bitterest engagements of the civil wars. In those two months until surrender on 28th August there was fierce fighting, heavy bombardments, and starvation of the town. Some 1500 people died, 186 houses were destroyed, and the garrison eat its 800 horses. The aftermath was a huge fine for the town, executions and exiles to the West Indies.

Sir Thomas Barnardiston of Kedington led one of the infantry regiments on Parliament's side in the siege.

Much of England, including many Puritans, were appalled by the King's execution. They had only wanted to get him to govern with Parliament, not to remove him. Even senior activists like Nathaniel Bacon of Ipswich were in despair.

England now became a republic. In March the Monarchy and the House of Lords was officially abolished. The Anglican church was also abolished and people were no longer fined for not attending their local church. However, everyone was still expected to attend some form of religious worship on Sundays.

The Commonwealth was declared in June, and would last until 1660, an eleven year constitutional experiment.

In April 1649 the lands seized by Parliament from the Cathedrals was sold off. The Bishops' land had already been sold off in 1646. In July 1649 the Crown lands were sold to raise money. The post civil war period was the greatest transfer of land since the Dissolution of the Monasteries. Men like Ralph Margery of Walsham le Willows came out of the war on the victorious side, and was able to buy crown land in Bedfordshire and Lincolnshire. Another Roundhead soldier, John Moody of Bury St Edmunds, also bought crown lands.

Other Suffolk men got land in Ireland, having invested in its re-conquest in an arrangement in 1642. Sir Thomas Barnardiston of Kedington got 2,221 acres. Samuel Moody, a cloth merchant in Bury St Edmunds got 888 acres in Ireland, and lesser areas went to Philip Sparrow of Wickhambrooke, and John Fiske of Rattlesden.

Their most famous member of the sect known as the Ranters was Laurence Clarkson or Claxton, who joined the Ranters after encountering them in 1649. Under the influence of the Ranters, Claxton published his 1650 tract called "A Single Eye" in which he espoused the dissenting group's ideals. Clarkson opposed the idea of sin, considering it to be "invented by the ruling class to keep the poor in order." He felt that only the intention of an act, and nothing at all about its content, mattered to God.

After claiming to have had spiritual revelations, beginning in 1651, Muggleton and his cousin John Reeve announced themselves as the two prophetic witnesses referred to in Revelations 11:3. Their book, "A Transcendent Spiritual Treatise upon Several Heavenly Doctrines", was published in 1652. Muggleton was imprisoned for blasphemy in 1653, and his own followers temporarily repudiated him in 1660 and again in 1670. His attack on the Quakers led their leader, William Penn, to write "The New Witnesses Proved Old Hereticks" (1672).

The Quakers had at first been a north of England movement, and in 1654 they sent a "mission to the south". Two quaker preachers duly arrived in Suffolk, and probably came to Haverhill. They were Richard Hubberthorne and George Whitehead, and although the east of England was "stony ground for Quakerism", they started a small group in Haverhill. Anthony Appleby was the most prominent of this small group.

On 6th July, 1654, John Lanseter, who had been a founding figure of the Independent movement in Bury St Edmunds and main signatory of the 1646 Covenant, was ejected from his own church for the sins of drunkenness and uncleanness. The record stated that "John Lanseter a member of this church, one of the foundation, for divers years an useful instrument for the good of the church, afterwards falling into the heinous and beastly sins of drunkenness and uncleanness was at length with great sorrow and lamentation when the whole church was met together, delivered over into the hands of Satan and cut off from the body about the 6th day of the fifth month commonly called July in the year of grace 1654."

The Quaker missionary Francis Howgill wrote in July 1655 that he held meetings in Norwich, Ipswich and Edmundsbury. One of the little rebellions of Quakers was to refuse to use the word saint, so St Edmundsbury would be called only Edmundsbury. Whatever the name, this is the the first evidence of quakerism in Bury St Edmunds. Unlike the reception in 1654, Howgill wrote that "Many large and great meetings we had....and we kindled a fire in that country."

Some other Quakers were arrested at Bures and two men, George Whitehead and John Harwood, were imprisoned in Bury gaol.

At this time the gaol in Bury was opposite the Corn Exchange, on the site of today's MVC Music and Video store. Today it would be described as being on the corner of Woolhall Street and Cornhill. They described it as "a low dungeon-like place, under a market house, our poor lodging being upon rye-straw on a damp earthen floor." For protesting against the conditions they were moved into a deeper dungeon, about four yards deep underground reached by a ladder. It had "but a little compass at the bottom and in the midst thereof an iron grate, with bars above a foot distant from each other and under the same a pit or hole, we knew not how deep". This gaol was eventually pulled down in 1770.

In Bury similar persecution of Quakers had also continued.
Following an appeal to Cromwell himself, the Lord Protector made an order to release all 'Friends' in prison at Bury St Edmunds, Colchester and Ipswich. In all, thirty-three Quakers were set free in Bury. They included men like George Whitehead, who seemed to have been held since the arrests of 1655, and even one man, William Burroughs, of 80 years of age.

Charles II was recalled unconditionally and he would rule until 1685. When Charles II was placed on the throne in May 1660 this event became known as The Restoration of the Monarchy. This came as a surprise in many parts of the country.

Along with rewards came some retribution. In Suffolk about 23 to 25 puritan clergy who had been intruded into their livings under the Parliamentary regime were evicted to reinstate the old incumbents. At Long Melford, the high churchman Robert Warren was reinstated to his living in May 1660, despite being 96. By November he voluntarily resigned his situation with a request that he be succeeded by Nathaniel Bisbie. Bisbie was probably also high church and thus immediately unpopular with a large section of his more "godly" congregation. He also attempted to reimpose all his tithes and dues of which the records had been destroyed by the mob in 1642. Bisbie was to leave behind him a considerable documentation of life and times for the parson at Long Melford in these years with the aim of protecting the rights of future holders of his office. Bisbie was himself to lose his living when he refused to swear allegiance to William of Orange in 1690.

The so-called Cavalier Parliament was elected in April 1661. They passed a series of laws called the Clarendon Code, starting with the Corporation Act, 1661. They wanted to rid the boroughs of those Puritans who had elected the old Parliament.

After the reign of Charles II (1660 to 1685) witches were still brought to trial, but were no longer executed. The witchcraft laws were not finally abolished until 1736.

The year 1662 has become known as The Great Ejection followed the Act of Uniformity of 1662 in England. The Act of Uniformity prescribed that any minister who refused to conform to the Book of Common Prayer by St Bartholomew's Day (24 August) 1662 should be ejected from the Church of England.

Several thousand Puritan ministers were forced out of their positions in the Church of England, following The Restoration of Charles II. Although there had already been ministers outside the established church, the Great Ejection created an abiding concept of non-conformity.

Against the King's wishes, Parliament had passed the Act of Uniformity. This made the Church of England the official religion and all other denominations were forced underground. Puritans in the church were no longer tolerated.

The Church of England was restored along with its Bishops and Hierarchy. Having already evicted those clergy who had previously replaced evicted Anglican rectors, those puritan clergy who had always held their livings were now targetted. Some 56 ministers were evicted in Suffolk under this legislation, as well as the 23 or so, evicted in 1660.

The newly appointed Bishop of Norwich was Dr Edward Reynolds. He would be Bishop from 1661 until 1676, and had been a Presbyterian in the past. Although he followed the law in action against puritan ministers, he did not attempt to pursue them after eviction. Thus these dissenters were not persecuted as badly as they might have been.

As a result of the Uniformity Act, Stephen Scandarett, the fiery puritan preacher was ejected from his living at Haverhill. Scandarett was fervently anti-Quaker, even writing "An antidote against Quakerism". He had probably been behind incidents like the beating of the two Quaker preachers in 1656 in Haverhill. Scandarett may have continued to lead a clandestine congregation in the period from 1662 to 1672, when he would be licensed officially as a presbyterian preacher. This group represents the origins of the Old Independent Congregational Church, but the existing church of that name was not built until 1884.

Following the same Act, old Samuel Fairclough, a Haverhill native, but now Vicar of Kedington, was also ejected from his living at the age of 68.

These evictions and the legislation behind them, is the reason for the division in the Protestant church in this country between Church and Chapel.

The Quakers refused to meet secretly and instead, met in public. They therefore took the brunt of official action against all non-conformists, and would suffer in this way for many years. However, by 1662, most Quakers had turned to pacifism, so avoiding the arrests for disorder that had characterised their early years.

Some 39 licences were issued to Presbyterian ministers in the South and West of Suffolk while the Congregationalists were more prevalent in the North-East around Lowestoft. At Bury a license was issued to Samuel Moody to hold meetings of a Presbyterian congregation at his house in Abbeygate Street. John Clarke's home at Bury was also licensed.

Stephen Scandarett, expelled from his Haverhill church living in 1662, was now allowed to get a license to become a presbyterian teacher. The house of Joseph Addy became the presbyterian meeting place in Haverhill. This congregation would become the Independent Congregational church in the next century.

Some time in the 1670s the Jesuits probably quietly moved into the Bishops Palace in the Abbey Grounds, and this became the base for their College of the Holy Apostles. Not all Catholics welcomed the presence of Jesuits. The Short family had always been Church Papists, willing to attend services of the established church while remaining Catholic. The Jesuits were the enemies of Church Papists, seeing this as an abandonment of their religion.

Parliament was aghast at the king's action on religious toleration, as was much of the population.

The Compton census of 1676 measured the sizes of the minority religious congregations. Wattisfield had 49 independents and Hepworth had 37. Bury had 167 dissenters and Clare had 300, Sudbury had 100, and Mildenhall had 66. The Bury non-conformists were divided across the existing parishes within the town. The parish of St James held 53 of the total number and St Mary's parish contained 114 of them.

As for Catholics, these tended to be clustered around local gentry families of that religion. There were 16 at Stanningfield, around the Rokewoods. There were 30 at Long Melford which had the Catholic gentry Martin, Harrison and Hinchlow families. Wetherden seems to have been the exception to this rule as this village had 18 Papists, with no local member of the gentry to protect them.

Some Catholics blamed the uncompromising attitude of the Jesuits for the persecution. At Bury, Richard Short junior was one of their most prominent critics, and subscribed to the idea that Catholics ought to swear an Oath of Allegiance to the monarch. Jesuits refused this idea because the monarch claimed to be Head of the Church in England, ahead of the Pope.

The motive for the attack was the King's sympathy towards the Catholic religion, and his brother's known conversion to Catholicism in 1673.

The Catholic James II came to the throne, and in his short three year reign he aimed to free Roman Catholics from the legal penalties imposed upon them by current laws. He had hoped that his presence on the throne would encourage the people to return to Catholicism of their own accord. But he had not understood how much the people were still suspicious of that religion and what it might mean for their future.

The anti-Catholic laws remained in place, but were unenforceable without incurring the new King's displeasure.

Emboldened by a Catholic sympathising king, the East Anglian headquarters of the Jesuit College of the Holy Apostles was more formally established in the Abbey Ruins in St Edmundsbury. The Abbot's Palace was probably purchased and new building work was carried out. These improvements were to be short lived, and destroyed by a mob in 1688. The College of Holy Apostles had been set up in 1633 to provide for the needs of Roman Catholics in the eastern counties. Sometimes clandestine, often peripatetic, it had very likely been in Bury St Edmunds since the 1870s.

For a brief period until 1688 the Town Corporation included Catholics, and Non Conformists as well as Anglicans. One such councillor was Dr Richard Short, who lived in Risbygate Street. The Shorts had always been "Church Papists", which meant that , although Catholic, they were prepared to attend the Church of England services, and thus avoid the penalties levied on recusants.

The Shorts came to Bury in the 1590s from Timworth, and there were several branches of the family. They were always Catholic, and usually followed the medical profession, having to qualify abroad because of their religion.

Because of their willingness to compromise over church attendance, the Shorts were opposed to the Jesuits presence in Bury St Edmunds. They opposed the new school and instead applied pressure on the Bury Grammar School to admit Catholics. Thomas and Richard Short served on the Bury Corporation, along with the new Catholic Mayor John Stafford, whose brother Nathaniel was a Jesuit.

On 29th June the courts acquitted all the bishops to tumultuous public acclaim. Clearly the King was getting nowhere with his religious toleration policies using current tactics.

By now King James II was starting to enforce his will on local corporations to force them to adopt Catholic MP's, or at least, anti - Tory MP's. Lord Dover, the King's agent in this matter, sent the St Edmundsbury corporation a royal instrument ordering that 16 named members would be replaced by Crown appointees.

While this was happening, the King's second wife, Mary of Modena, had given birth to a son. The prospect of a Catholic dynasty spurred on Seven leading Whigs and Tories to issue an invitation to William of Orange on 30th June to defend English liberty and the Protestant religion.

By October, it was clear that the country would not put up with any more of this. William of Orange landed in the country at Torbay, on the 5th November supported by his 20,000 strong army and those Englishmen who wanted to ensure England remained protestant. James retreated back to London and then became unwell and lost his nerve and attempted to flee the country, trying as he goes to throw the great seal of England into the Thames. The Crown's nomination rights lapsed when James II finally fled the country on 23rd December, 1688.

Crowds took to the streets to celebrate. Unfortunately the king had advanced the Catholic cause too hard, and there was now a backlash against Catholics. Riots ensued in London and various other places, including Bury St Edmunds, with Catholic chapels being the first targets.

In early December, 1688, the rabble of Bury St Edmunds joined the Cambridge mob in a march on Cheveley in Cambridgeshire. Here, Henry Jermyn, the First Baron of Dover and a great supporter of James II, had a Catholic chapel at his magnificent home in Chevely. The Catholic chapel was pulled down and the house was wrecked. The Bury mob went home and was quiet for a few days.

The Catholic Mayor of Bury, John Stafford, was now accused of trying to blow up the Guildhall. Such rumours were inflamed when another rumour that Irish soldiers were marching on the town was spread.

On 20th December the Bury mob went on the rampage again. The recently built Jesuit college, known as the Mass House, in the old Abbot's Palace in the Abbey grounds was their main target. Both Jesuit school and chapel were pulled down, stone by stone. The remains were set on fire until it was destroyed down to ground level.

One Catholic had been killed trying to defend the chapel and the houses of two Catholics were torn down by the mob before the local gentry halted the violence. The Jesuits fled to the house of Thomas Burton at Beyton and made no attempt to return to Bury.

The mob, who were described as the Mobile, ie vagrants and paupers, now roamed the streets of Bury looking for more targets. The homes of several Catholic members of the old corporation were ransacked, including John Stafford's. However, newspaper reports at the time said that they also rifled both Papists and Protestants, Test Men and Anti-Test Men, without distinction.

Test Men were those who supported the Anti-Catholic Test Acts, and thus should have been immune in these riots.

About 10 people were said to have died in these riots in Bury before the Magistrates restored order, imprisoning those they could catch.

Roman Catholic worship did not come out in the open in Bury again until the Westgate Street chapel was built in 1760 - 1762.

With the new royal family come permanent toleration for nonconformist Protestant religions, by way of the Toleration Act of 1689. Suffolk was a stronghold of nonconformity and its practitioners now became established and respectable. However, some clergy refused to swear allegiance to King William. They were called the non-jurors and about 23 Suffolk clergy were evicted for this offence. Three were in Long Melford, the rest spread across the county. The Melford evictions included Nathaniel Bisbie, who is known to us for his extensive documentation of the transactions of his living, and of local conditions. He died in 1695.

Nationally the Non-Jurors were Archbishop Sancroft and his six Bishops, and 400 lesser clergy, including the 23 in Suffolk.

William Sancroft was born in Fressingfield in Suffolk in 1617, but was educated at Bury St Edmunds Grammar School and at Cambridge university. He was a Royalist, and was Dean of St Pauls when it burnt down in 1666. He became Archbishop of Canterbury in 1678 and had resisted King James' Declaration of Indulgence in 1688, being imprisoned for it. But he felt it was wrong to de-throne a King in principle. He was suspended from office and evicted from Lambeth Palace. He returned to Fressingfield and lived like a hermit in a poor cottage until he died in 1693.

Other supporters of King James in exile were called Jacobites, and Norwich was a centre of East Anglian Jacobitism. Suffolk had few Jacobites apart from the religious Non-Jurors.

Most of the old Presbyterians had gone back to the official church after the Restoration, but a few had quietly kept to Presbyterian ideals. After the Toleration Act they started to build a Meeting House at the top of Churchgate Street. However, this is not the building which we see today, which came in 1711. They could do this provided they got a license from a JP.

The Toleration Act did not allow freedom of worship to Catholics, Jews or Unitarians. Neither did it allow Dissenters to hold public office or become MP's. They were still second class citizens. However, this amount of toleration was ahead of the continent, and was acceptable to the bulk of the population.

"the Shorts took advantage of the vacuum, and in 1691 they established a town mission led by a secular priest (meaning he belonged to no religious order) called Hugh Owen. Owen, who was born in the Isle of Man, remained in Bury until his death in 1741. In the early days, he may have ministered from the Short family home in Risbygate Street, but by the 1730s he was based at the Greyhound Inn on Cornhill, which later became the Suffolk Hotel and is now divided between Waterstone’s and Edinburgh Woollen Mill.
The Greyhound was owned by a Catholic landlord, William Adams. Owen sometimes also ministered at the Angel and at a coffeehouse called Hannibals."

Her mother was strongly non conformist and Celia inherited the family outlook on religion and whiggish politics.

Her stop at Bury was thus just one more small town on her grand tour. She thought 'the prospect was wonderful pleasant,' and 'there are a great deal of Gentry which lives in the town.' She also noted that there were many dissenters in the town, with 4 meeting places including those for the Quakers and Anabaptists.