The earliest reference to a church at Whaddon is between 1110 and 1122 when Henry I made a grant of the church at Alderbury to the Bishop of Salisbury. The grant included a chapel at Whaddon. In 1272 the church, as part of the Manor of Whaddon under the lordship of Alan de Plugenet, was valued at 7 marks per annum. In 1328 the Manor was passed to the Priors of Ivychurch and in 1394 it is recorded that the Priors were required to say mass at the church three times a week. It is not known when the church fell into disuse but it was not recorded in an inventory of Ivychurch Priory undertaken by the Royal Commission of 1536. It is believed that the church was located at Whaddon Farm.