St Margaret's has a nave with a broad N aisle and a narrow S aisle, a chancel with a N aisle partly partitioned off to form a vestry, and a W tower with a broach spire. The oldest work here is a series of Anglo-Saxon reliefs related to those at Breedon-on-the-Hill (Leics) and now set in the E chancel wall above the altar (until recently they were outside, built into the E buttresses). The N arcade, N chancel arcade and chancel arch all date from c.1160; the S aisle was added c.1300 and it was probably at this time that the N aisle was widened, and the two W bays of the N arcade turned into a single long bay by removing a pier and building a broad arch. In 1872 the church was restored and a S porch built, and in 1901 the N aisle was again rebuilt and extended to the E end of the church, absorbing the chapel and vestry that were there before. The spire was struck by lightning in 1917 and the upper part had to be rebuilt. The nave, chancel and S aisle are faced with stone rubble; the N aisle is of rough-faced ashlar; the lower storey of the tower is of rubble and the upper storey of roughly-coursed ashlar blocks. 12thc. work is found in the S chancel corbel table, the N arcades of nave and chancel and the chancel arch. 2 fine relief panels showing standing figures, built into the S wall of the chancel, are probably 9thc., but are described and discussed since they have sometimes been dated to the 12thc.

A confirmation of the grant of lands to Peterborough (Medeshamstede) by Wulfhere, king of Mercia, in the same year includes Fletton, but this is generally thought to be a post-Conquest forgery. It was still held by the Abbot of Peterborough in 1086, and the manor included a church at that time.

The two figural reliefs are the subject of some disagreement. First it should be said that they are stylistically related to the relief at Castor supposed to come from St Kyneburgha's shrine, which has the same treatment of heads, of drapery, especially around the hem, and similar feet. The presence of the earlier frieze at Fletton, which is indisputably linked to the Mercian work at Breedon on the Hill (Leics) has led most scholars to suppose that these figures are from the same early period. Clapham (1927), 235-56, dated them to the late 8thc., as part of a group of Mercian works centred on the Hedda stone in Peterborough Cathedral. His view has been more or less accepted by the majority of scholars, including Gardner (1951), 38. Kendrick (1938), 176-78 and Tweddle (1991), 239-40 preferred an early 9thc. date, and Stone (1955), 24, a date in the mid-9thc. Rice (1952), 88 was unable to decide between the late 8thc. and the early 10thc., but had a slight preference for the former. RCHME preferred the later date, 'perhaps 10th-century'. As early as 1927, however, the President of the Society of Antiquaries (David Lindsay, Earl of Crawford) expressed a preference for a 12thc. date for these reliefs.

A curious position was taken by Pevsner (1968), who related the Fletton figures to 'French sculpture of the early C12' while attributing the obviously related Castor stone to the mid-9thc. The treatment of hair is certainly classicizing, and the drapery patterns, especially on the apostle figure, have the kind of schematised fold pattern for which a date in the 12thc. would be perfectly acceptable. However, neither on these reliefs nor on the Castor one is there anything diagnostically Romanesque. The Castor figures stand under fictive arcading, and the capitals relief have an Anglo-Saxon bulbous form while the book-cover held by the main figure is decorated with a knotwork design. The present author remains unsure, but on balance leans toward the view that these are Anglo-Saxon, and from a period exposed to Carolingian classicism, i.e. probably the early 9thc. Multi-scallop capitals with cusped shields also occur at Upwood, and in more complex forms at Denny Abbey and Ely Infirmary. The corbel table resembles the one reset at Little Stukeley.