In Madingley Hall there is a stained glass window which says "Who Stole Histon Church?, this refers to Histon St Etheldreda's.

Histon's second parish church, St Etheldreda's, stood about 400 yards to the West North West of Histon St Andrew's and was probably of late Norman origin. It had its own parish and manor and probably originally looked much like the Leper Chapel on Newmarket Road. Until the Dissolution of the Monasteries (1536-40), it belonged to the Abbot and Convent of Eynsham in Oxfordshire and at one time was probably larger than its sister church, St Andrew's, as in the 13th century it was assessed at 20 marks compared with the 10 of St Andrew's. At some stage St Etheldreda's had a tower added and in 1549 there is reference to a chaplel dedicated to St Nicholas.

By 1588 St Etheldreda's was in a poor state of repair, though it was still a working church, with the Rev Johannes Harrison as the Vicar. Shortly afterwards Sir Francis Hindi, the owned St Etheldreda's Manor, had the church pulled down as he wanted some materials to enlarge Madingley Hall. He left just the chancel, where two former vicars had been buried: William Vale in 1491 and John Hopkyne in 1501. The rest of the materials he used or used off. As a result of this the two parishes of St Andrew's and St Etheldred'a became one with the Rev John Jackson become the first vicar of the united parish.

Later in 1638 enquiries were made about re-building St Etheldreda's but the cost would have been to much, so the idea was dropped. By 1745 all signs of the church, including the chancel which had still be standing in 1728, had gone and today all that remains are a few bumps in the ground which are on private land at Abbey Farm. The churchyard of St Etheldreda's survived until about 1727 at which time it was incorporated into Abbey Farm.

The font at Madingley, which is late Norman in date, is said to have come from St Etheldreda's and it is said that the spire at Madingley also came from Histon but the latter seams unlikely. What is for certain is that some of the carved stones from St Etheldreda's, probably roof supports, were returned to Histon and today can be found on the window shelves in Histon St Andrew's.