The nave of Aldingbourne has a blocked N arcade, with traces of 12thc. or 13thc. painted geometric decoration on the face of the second arch from the W and on the soffit of the doorway in the westernmost bay. Traces of a Norman window can be seen in one of the S arcade spandrels. The E bay of the S aisle is roofed with a rib vault and has crocket capitals and dogtooth mouldings. A tower was built on the N side of the church in the 13thc. The chancel is the same height and width as the nave, and has a vestry on the S side.

A monastery was established at Aldingbourne in the 7thc. Aldingbourne church is mentioned in the Domesday Survey, as a possession of the Bishop of Chichester; it had previously been held by his predecessor, the Bishop of Selsey. The monastery appears to have become the Bishop's Palace, which was destroyed in 1642-43. Aldingbourne church formed part of one of the richest prebends of the cathedral and in 1227 was assigned by the Chapter to the Dean of Chichester. The N arcade was blocked c.1350, with material which included fragments of Sussex marble tomb slabs. The church was restored by Ewan Christian in 1867 (the date on the rainwater head of the vestry), and at the same time the S aisle was rebuilt. According to Peat and Halsted, there was an earlier restoration in 1850. Clayton, writing about a later 1889 restoration, noted the discovery (beside the S door in the E wall of the porch) of the 'remains of what may perhaps be a holy water stoup' and, behind deal paneling in the chantry chapel, 'a sadly mutilated piscina' (Clayton 1890,191). It is not clear which of these is represented by the fragment described above (V.3.). A notice beside the mortar reads: 'believed to be the font of the ancient chapel of Lydsey and to date back to Saxon times'. The evidence for the connection with Lydsey is not known.

'a tall and very beautiful image of the blessed Mary' was bequeathed by Dean Roger de Freton in 1382.

C. E. Clayton (SAC 12, 1860, 61) notes that the dedication to St Mary is recorded in 1479.

The S arcade appears to date from c.1200, but the vaulting of the E bay, which has been compared with late 12thc. work at Chichester Cathedral, is probably slightly later (Nairn and Pevsner 1965, 77-78). The font, of a common regional type, dates from c.1175-1200.