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). In 1706 the return noted that of fifty families on the parish, six or seven were nonconformists "chiefly Quakers. No Meeting house, no Papist or reputed Papist in the parish". Three years later the numbers of nonconformists had risen to eleven or twelve families "of Quakers and Anabaptists [Baptists]". In 1712 the number had decreased again to five or six families. These widely varying seem to suggest an Anglican clergyman not interested enough to get the numbers right, or that the nonconformists were secretive in their allegiance, fearing persecution - or, perhaps, both. By 1717 the number of dissenting families was given as ten "chiefly Quakers but some of the Antipaedobaptist [against the baptism of children] perswasion [sic]". There was still no meeting house in the parish, as was the case in 1720, when five families were stated as being Quakers and two Antipaedobaptists.

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. The one registration for Totternhoe that cannot be definitely allocated to a denomination is one made in October 1834: a farmhouse, open field and little meadow of James Purton, occupied by Henry Purton were registered by Henry Purton himself, Joseph Holland, John East, William Jeffs and William Tompkins [ABN1/2 and 2/296]. Surprisingly no buildings owned by James Purton or occupied by Henry Purton are mentioned on the parish-wide survey of 1829, though Henry and James Purton are shown occupying cottages owned by other people in Church End and another James Purton is shown occupying a cottage owned by someone else opposite what is now 188 Castle Hill Road.