As Pepperstock lay in Hertfordshire until 1965 Bedfordshire & Luton Archives & Records Service does not have many sources for the Baptist Church, just a series of correspondence with Slip End Methodist Church [MB1759] and some mentions in a booklet called "The People of the Meeting House" written by J. S. Fisher in 1976.

Fisher's book notes that Baptists were meeting in Pepperstock as early as 1817 when the Bedfordshire Union of Christians noted that "Brother [Ebenezer] Daniel, of Luton, and the members of his church, preach at Sundon, Streatley, Lilley, Coleman Green, Stopsley and Pepperstock". Meetings were obviously held in the evenings on occasion as Fisher notes that the meeting held candle collections, raising 6/6 in the winter of 1829/30.

J. S. Fisher also notes that Pepperstock was flourishing in the 1850s with a growing Sunday School, which would have taught such things as reading and writing as well as religious topics for which Sunday Schools are reserved today.

In the early 1970s Pepperstock Baptists obviously had good relations with the Methodists in Slip End as it was proposed to sell the Slip End Methodist chapel and enter into an agreement to share Pepperstock Baptist chapel. This proposal was made following an inspection in 1972 by chartered architect Clifford W.Shrimplin reported on both premises.  Of Pepperstock Baptist chapel he said: "A brick and slated building about 70 years old of very similar characteristics to Slip End Church, except that the main roof is probably in a slightly better state of repair. the work and cost necessary to put the premises in a reasonably good state of repair is almost the same as required for Stony Stratford Church".

He concluded "I understand that the location of each church is relatively unimportant as regards distance from the centre of the village as in any case the straggling nature of same makes the definition of  "centre of village" difficult. I would have thought, however, that Slip End was a little better sited in relation to public transport, but that there would be less noise at Pepperstock. To sum up, I would recommend that Pepperstock be retained and Slip End be sold. My principal reason for suggesting this is that whereas any alternative use for Pepperstock would, in my opinion, be refused permission by the Planning Authority and therefore become valueless, the redevelopment of the Slip End site for say residential purposes could not be refused. The money from the sale of same could be used to create good and acceptable conditions at Pepperstock". The decision was duly taken by the Methodists to sell and the chapel was sold in 1973, Slip End/Pepperstock becoming only the third instance of Baptists and Methodists sharing a building in England.