In 972, an Abbey was re-founded by St Aethelwold and run strictly in accordance with the Benedictine Rule.  It became the centre of a major fenland estate and large stone buildings were built to glorify God as they were at nearby Peterborough, Crowland, Ely and Ramsey. 

The large Norman church, built from 1080, contained the relics of important saints such as St Botolph (brought from Boston) and attracted visitors and their donations.  Further buildings were added and embellished, especially from 1305 to 1323, but The Black Death of 1349 killed 13 of the monks and 100 people in their household.

At the Dissolution of the Monasteries under Henry VIII, Thorney still had an abbot and twenty monks, and an annual value of £411 12s 11d.  The monks were given pensions and the Abbot retired to Whittlesey.  The  Abbey was rapidly stripped of many building materials, some of which went to Cambridge to build college chapels, and the Abbey's church was reduced to a ruin.  By 1550, the island of Thorney and its surrounding fens were granted to John Russell, 1st Earl of Bedford.

An archaeological survey in Church Street has uncovered remains of the building steel used in this 'asset stripping'.  This included the remains of a furnace used to melt the lead from the stained glass windows.  Fragments of medieval stained glass were also recovered.