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 Silsoe is included with that for Flitton, since Silsoe was, at that time, a hamlet of Flitton. The information includes the following:

• 1706: the parish contained 150 families: "Out of these are but 3 Dissenters, two of them Anabaptists [i.e. Baptists], and the third a Quaker. They have no Meeting house within the parish.
• 1709: out of 580 inhabitants 7 were Baptists and 4 were Quakers.
• 1712: of 139 families in the parish there were two families of Presbyterians.
• 1717: of 140 families in the parish there was just one of dissenters, who were Baptists. There was no meeting house.
• 1720: of 140 families there were two families of Presbyterians, with no meeting house.

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 Silsoe:

• 1794: the dwelling house of Catherine Studman, widow registered by the widow herself and John Hickling, Jonathan Clark and James Schofield [ABN1/1; ABN2/73]. It seems likely that this is the large room referred to in a letter from schoolmistress Sarah Harrison  - it was taken by a Methodist preacher;
• 1802: the dwelling house of James Chapman [ABN1/1];
• 1806: the dwelling house of William Austin registered by Austin himself, John Aikenhead, John Bedford and James Chapman [ABN1/1, ABN2/122];
• 1808: the house of James Chapman again [ABN1/1];
• 1824: a house in the occupation of Mrs. Whitbread registered by Samuel Hobson of Maulden [ABN1/2, ABN2/208, ABN3/3].

No purpose built nonconformist chapel was ever built in Silsoe. This was largely down to the attitude of the Earls of Kent and their successors, the Earls de Grey and Barons and Baronesses Lucas of Crudwell. The family owned the Wrest Park Estate until the end of the First World War and, with it, most of the village. They were Tory in their politics and thus fervent supporters of the Church of England and opponents of nonconformity, whose cause was championed by their political rivals the Whigs.

In 1811 Lewis Harrison, Silsoe agent for Amabel Hume-Campbell, 5th Baroness Lucas and, from 1816, 1st Countess de Grey wrote that he had bought a house in West End Road for 250 guineas "to prevent the erection of a Methodist chapel which would certainly happened had it been sold to Croxford or Flint who were bidding hard". He could "get rid of it if your ladyship pleases" [L30/11/108].