What survives of the abbey church begun under Gunter, abbot from 1085, is the five W bays of the nave, with alternating round and compound piers, divided into bays by half-column responds running up from floor to ceiling, where they terminate in a cornice, presumably of 1638. The nave was originally aisled and had a gallery and clerestorey. The aisles have been demolished and the arcade walled below and glazed above. Likewise the gallery arches have been glazed and the roof lowered by the removal of the clerestorey (although the blocked windows of the W bay survive, visible on the exterior). The arcade and gallery arches are thus visible both inside and out. All this remodelling work dates from the rebuilding of 1638. At the W end the Norman buttresses have become the twin turrets of a 15thc. façade, with a Perpendicular W window and doorway. At the E a transept copying the Romanesque work, with vestries and organ in the arms and the altar in the centre, was added by Edward Blore, architect of Buckingham Palace, from 1839-41. Thorney was in Cambridgeshire until 1965, when it a boundary change moved it to Huntingdonshire. It reverted to Cambridgeshire when Huntingdonshire was abolished in the 1974 reorganisation.

This is apparently the third monastery on the site. Saxulf, first Abbot of Peterborough, was said to have built a hermitage here c. 662. This was destroyed by the Danes (c. 870), to be refounded a century later (972) by Aethelwold. The dedication was to St Mary, although the nave (Holy Trinity), W end (St Peter) and N portico (St Benedict) had their own dedications too. The present double dedication seems to date from shortly afterwards, connected with the acquisition of St Botolph's bones. Aethelwold's church was taken down by Abbot Gunter (1085-1112) who began the present building. The church was advanced enough for the monks to enter it in 1098, and the whole of it was complete by 1108, although the dedication was not for another 20 years. In 1086 Thorney was a major landlord, with holdings in Cambridgeshire, Huntingdonshire, Bedfordshire and Northamptonshire. According to Knowles's calculations on the Domesday Survey it ranked 36th in wealth among abbeys, with a value of £53.15s. This may be compared with the figure of £768.17s.3d. for Ely, the second-ranked house.

The nave arcade capitals range from extremely crude and massive tectonic forms to simple multi-scallops with some variety in the treatment of angles and inter-scallop features. The round piers are consistently given simple cushion or tectonic capitals, and the more avant-garde forms are confined to the compound piers piers. In the gallery the predominant form is the volute capital, sometimes of the Ely type, in which the volute forms the tip of a leaf on the angle. This occasionally transposes into a flat-leaf form. Much more virtuosity is displayed here, but it is instructive to find what is conventionally considered to be the stylistically earlier capital form at a higher level, and therefore presumably later in absolute date. Pevsner (1968, 351) and Fernie (2000, 176) observed that the piers are dependent on the (contemporary) nave of Ely. Rigold (1977, 103) related the sawtooth bases to those at Castor. Similar undivided gallery openings are found at St Botolph's, Colchester (Essex).