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 Leighton Buzzard includes the following:

• 1706: "In the whole parish of Leighton [including the modern parishes of Billington, Eggington, Heath & Reach and Stanbridge] is only one Quaker, and about 40 Anabaptists [Baptists], who have 2 Meeting houses, one in Leighton, the other in the hamlet of Heath & Reach. No Papist, or reputed Papist, any where in this parish";
• 1709: "Dissenters in Leighton about 39; Eggington 2; In Stanbridge 9. Most Anabaptists, some Quakers. In Leighton an Anabaptist meeting once a fortnight. Their number seldom exceeds 40";
• 1717: "about 15 [families of] dissenters called Anabaptists…There is a private house, the dwelling of William Fenner, Licensed for such a separate congregation. The teacher's name is John Rouse senior preparing, 'tis said, to be succeeded by his son John Rouse, both of them very indifferently skilled in the handycraft trade of Shoemaking";
• 1720: "…between twenty and thirty of them [families] are Anabaptists, and one woman is a Quaker…There are two houses where the Anabaptists meet, but I do not know that either of them is Licens'd"

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. Those for Leighton Buzzard are as follows:

• 17th April 1672 - a Presbyterian meeting in the house of Thomas Bryan [OR page 851];
• 20th July 1761: the house of Joseph Brooks was registered by William Brown, John Morris, John Bennell and Michael Morris [QSP43/3];
• 6th July 1798: the dwelling house and premises of Thomas Chew was registered by Thomas Chew, W.Emerton and John Procter [QSR1798/65];
• 12th April 1817: a "certain room" in the dwelling house of John Warner was registered by John Hodgson of Leighton Buzzard, preacher [QSR1817/286-287, QSM26 page 20];
• 24th December 1818: the house of Thomas Chew was registered by David Lee Willis, solicitor [ABN1/1, ABN3/3, 10];
• 18th September 1819: the wheeler's shop of Richard Lock, wheelwright was registered by George Row of Leighton Buzzard, minister [RI3/6821];
• 29-30th October 1830: the house of Thomas Shepherd in North End was registered by the owner [ABN1/2, ABN2/251, ABN3/3, 99]