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.

Volume 81 published by the Bedfordshire Historical Records Society (2002) is devoted to returns made during episcopal visitations to the county by the Bishop of Lincoln in the early 18th century, edited by former County Archivist Patricia Bell. One of the questions asked was the number of nonconformist families in the parish; the various responses were as follows:

• 1706: "Of these 5 [families] are of dissenters reputed to be Independents, but they have no Meeting house in this parish. Nor do any Papists, or reputed Papists live in it";
• 1709: No Papists. About 30 dissenters, followers of one Killingworth, who has a Meeting every Sunday at Southill. He teaches here about once a month";
• 1712: "...of which 10 [families] are of Dissenters, Anabaptists, and Independents. No Meeting, save at a funerall [sic] etc.";
• 1717: "...of these [families] about twenty Dissenters, chiefly Anabaptists. One Licensed Meeting-house Anabaptist. They Meet once a Month. What number is uncertain";
• 1720: "Eleven [families] of Dissenters, of what sort I cannot tell. I suppose Anabaptists. No Meeting house that I know of at present in the Parish".

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.

Volume 110 published by the Bedfordshire Historical Records Society in 1996 and edited by Edwin Welch contains registrations of Bedfordshire nonconformist meetings drawn from a number of sources. One registration was recorded for old Warden for a meeting house of an unnamed denomination in the house of Thomas Preston in 1778, registered by Preston himself and William Tansley [ABN1/1 and ABN2/46].