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 fifty families in the parish, of which nine were dissenters (three or four Quakers the rest independents). "There is no Licensed Meeting house in this Parish".
• In 1709 of the three hundred or so souls in the parish forty were stated to be Anabaptists [Baptists] and fifteen Quakers. "No settled meetings, but Rawlins sometimes preaches here as in Bolnhurst, and now and then the Quakers also meet".
• Twelve families, two or three Quakers, the rest a mixture of independents and Anabaptists were recorded in 1712.
• The figure was seven or eight families of Independents "or, rather Anabaptists" and two families of Quakers in 1717 with "No meeting house of any kind"; the report for 1720 being the same.

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 Colmworth are as follows:

• In 1725 when a house used for dissenting worship was registered with the Quarter Sessions [QSR1725/76], sadly the document is damaged and no names survive.
• On 19th December 1766 the dwelling house of Mary Fisher was registered by Russell Chapman of Colmworth, an illiterate husbandman and Thomas Lee of Great Barford, husbandman [ABN1/1 and ABN2/23].
• In 1810 the dwellinghouse and premises of William Wagstaff was registered by Wagstaff himself and by Thomas and William Calvert [ABN1/1 and ABN2/137].
• In 1830 the dwellinghouse of Robert Shimmon [Skinner] was registered by Shimmon/Skinner, who could not sign his own name and witnessed by Samuel Barley and John Fielding [ABN1/2, ABN2/248 and ABN3/3].
• In January 1841 the house of George Creamer was registered by Creamer himself [ABN1/2 and ABN2/351].
• On 12th April 1841 Charles Crowsley, along with George Cornish, registered Crowsley's dwelling house [ABN1/2 and 2/354].
• A year later a building belonging to Henry Shimmon was registered by Charles Parker [ABN1/1 and ABN2/364] and it is possible that he shared Robert Shimmon's religious ideas.
• In 1844 a building occupied by James Ashwell was registered by William Youle [or Gould] [ABN1/2 and ABN2/375].

Given that the only known nonconformist meeting in the parish later in the 19th century is that of the Primitive Methodists, it seems reasonable to suppose that at least some of the registrations above are by people of that persuasion.