In 1672 Charles II issued a Declaration of Toleration for Protestants dissenting from the Church of England; this had the effect of some dissenting meeting houses registering with the Secretary of State. The Toleration Act of 1689 enshrined the right of protestants to dissent from the Church of England and, once again, encouraged meeting houses to register voluntarily with local quarter sessions| and Anglican church. Registration provided protection against persecution, laying a duty of protection upon magistrates and so was popular with nonconformists. Most registrations were made with quarter sessions until the middle of the 18th century, presumably due to the mutual antagonism of nonconformists and established Church. However, from that point registration with the Church, via the local archdeaconry| began to become the favoured method, because the archdeaconry Registrar would issue a licence at any time rather than during the days each quarter when the quarter sessions met.

Bedfordshire & Luton Archives & Records Service has a reasonable number of registrations of nonconformist meeting houses in both the Quarter Sessions and Archdeaconry of Bedford archives. Registration continued through the 19th century even though persecution faded away - this was because registered buildings were allowed to claim exemption from parish poor rates, were exempt from control by the Charity Commission and were allowed to be licensed to carry out marriages. These things meant that registration became almost compulsory in practice for well established nonconformist meetings. This is fortunate for the local historian because sometimes the only surviving references to a nonconformist meeting occur as registrations. One drawback with the registrations are that they do not usually inform the reader of the particular type of denomination involved, though sometimes it is possible to infer it from other evidence.

Bedfordshire & Luton Archives & Records Service has a number of registrations with the archdeaconry of nonconformist meetings in Wootton, of which some were by undisclosed denominations, the first being in 1806 at the house of Daniel Cook [ABN1/1]. This was followed the next year by the house of Samuel Sheffield [ABN1/1] and three years later by the house of John Vaux, labourer, registered by John Curtis junior, Thomas Warren, John Thompson and Daniel Cook [ABN1/1 and ABN2/138].

In 1838, two years after the opening of the Baptist chapel Calvinists W.Masters, John Plowman, Jesse Masters, Robert Warren and Samuel John Deeble registered "Mr.Master's Granary" for worship [ABN1/2 and ABN2/321]. The Baptists in Wootton described themselves as of "Calvinistic sentiments" in 1853 (see Baptists in Wootton|) and so this group may have been, or later joined the Baptists; Bedfordshire & Luton Archives & Records Service has no other records of this group in Wootton.