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 the registrations of nonconformist meetings in Wyboston:

•  In 1808 Thomas Howkins registered his house in Wyboston.
• In 1821 Thomas Howkins, John Howkins, Thomas Emery, John Pratt and James Knight registered the house of John Pratt and desired "a licence to be transmitted through the medium of the Revd. Thos.King, bearer".
• At the same time Samuel Hodby, W.Law, T.Hewitt, James King and William Hall registered the house of Samuel Hodby in Wyboston.
• In 1841 Joseph Clerk registered a building in Wyboston.
• The next year Thomas Hewit and John Hewit both registered separate buildings.
• Interestingly a Mormon church was registered in Wyboston in 1848 [ABN2] in the house of Thomas Joise.