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 Flitton includes the following:

• 1706: the parish contained 150 families: "Out of these there are but 3 Dissenters, two of them Anabaptists [Baptists], and the third a Quaker. They have no Meeting house within the parish;
• 1709: "Families 135, Souls 580, of which 7 Anabaptists, 4 Quakers";
• 1712: "Families 139, of which only 2 of Dissenters, Presbyterians";
• 1717: "We have an hundred and forty Families in the Parish of Flitton cum Silso and but one of them Dissenters called Anabaptists. We have no Meeting house in our Parish";
• 1720: "We have about an hundred and forty Families in our Parish, two of which are dissenters who call themselves Presbyterians. We have no Meeting house in our 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.

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 the following for Flitton:

• 22nd July 1672: the house of Elizabeth Hawkins at "Fleethaven" was registered;
• 24th October 1799: the house of John Brightman was registered [ABN1/1];
• 24th July 1818: the house of William Row was registered [ABN1/1; ABN3/3, 4];
• 17th November 1821: the house of John Thompson was registered by Thompson himself, Joseph Clarke and William Row [ABN1/2, ABN2/187, ABN3/3].