Before leaving the seventeenth century it is interesting to try and discover the extent to which religious life at Clare was affected by political happenings in the time of the Civil Wars and Commonwealth.
Suffolk as a county was already much affected by Puritanism in Elizabeth's reign. At that time an attempt was made in some localities to reform the church from within by means of a parish presbytery, composed of minister, elders, deacons and widows. The ministers of twelve parishes were to form a classis, with delegates to a provincial assembly which in turn was represented on a national assembly. At Dedham such a classical system was working, but it was not general. In the mid-seventeenth century, however, there was a more drastic scheme, which aimed at setting up a Presbyterian Church in place of the Anglican Established Church.
To this end in 1648 Suffolk was divided into fourteen divisions and Clare was the centre of the division which coincided with the hundred of Risbridge. It is not easy to find out what practical changes were effected. Vestry meetings continued, with their main function of auditing the accounts of parish officials; but very few inhabitants attended, and those present, Roger Cook, the minister, Giles Barnardiston, Francis Crosse the clothier and others, seem to have been of the Presbyterian faith. It is interesting to find that all officials, even the churchwardens, were elected in the court leets during these years, as if the headboroughs were dissatisfied with the Presbyterian influence in the church and hoped thereby to keep a balance. Whatever the religious changes, however, they were short-lived. For with the Restoration of Charles II in 1660, the old influences regained control and the Presbyterian ministers were ejected. Among them was Francis Crow, vicar of Hundon, ejected in 1662. He later moved to Ovington, where he was licensed to teach in his own house, then to Clare. For a brief time he was in Jamaica, but returned to die in Clare in 1687. Others like him remained true to the Presbyterian faith - Giles Barnardiston, Richard Cutts, John Bridgman and William Bareham all received licenses to teach, and in 1690 Philip Havers had a barn conventicle in Clare and baptised many private houses.
There was a strong Quaker influence in the town at the end of the seventeenth century; and a cottage at the foot of the castle mound, behind the moothall, was to be held in trust for the use of those of the Quaker faith. The first Congregational Church replacing the Presbyterian conventicle was build in 1710 on the site of the present Church, erected in 1841. The Baptists had a Chapel (rebuilt in 1859) soon after their coming to Clare c.1800.