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.

Visitations by the Bishop of Lincoln to Bedfordshire in the early 18th century give some idea as to the number of nonconformists in each parish from returns made by the vicar or rector. Former County Archivist Patricia Bell has compiled returns from 1706 to 1720 for the Bedfordshire Historical Records Society (Volume 81, published 2002); information for Wootton includes the following:

• 1706: “It [the parish] contains 80 families, of which some are Dissenters, cheifly [sic] Quakers. No Papists nor reputed Papists;
• 1709: “Families 58, Souls about 307. No Papists. 3 families of Quakers. No other Dissenters. No Meeting”;
• 1712: “Families 115. About 8 of these Dissenters, of which 4 Quakers. The rest part dissenters, part otherwise”.
• 1717: “Families about a hundred and twenty three. There are about ten families of all which some are Dissenters. There are three of those families Quakers. Meeting houses None”.
• 1720: “Ninety Eight Families, Four whereof are Quakers and Six Independents or Anabaptists. No meeting House”.

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.

Edwin Welch researched the history of registrations in Bedfordshire for Bedfordshire Historical Records Society Volume 75 Bedfordshire Chapels and Meeting Houses [published in 1996] and found that a Calvinist Meeting was registered in January 1838. This meeting was held in “Mr. Master’s Granary” and those registering were W. Masters himself, John Plowman, Jesse Masters, Robert Warren and Samuel John Deeble [ABN1/2; ABN2/321]. Other registrations can be attributed to the Methodists or Baptists.