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The dedication of the church of St. Margaret was originally St. Mary, and, down to the inclosure, part of Lewknor town field was still known as St. Mary furlong. The adoption of St. Margaret as patronal saint no doubt derives from the holding of the village wake upon St. Margaret's day.

The church is built of local flint with stone dressings, and comprises a chancel, nave, south aisle, and porch, a north transeptal chapel, and a western tower. Until the beginning of the 14th century it appears to have consisted of chancel, nave, and transeptal chapels all dating from the end of the 12th century. Of this late Romanesque church there remain the chancel arch, portions of the nave, the northern transeptal chapel, and the eastern respond of the arch to the southern transeptal chapel, now incorporated in the arcade of the 14th-century south aisle. The nave was lighted by lancets, of which two survive at the west end. Externally a portion of the original corbel-table can be seen on the south side of the nave towards the west end. The cylindrical font carved with a pattern of linked roundels also dates from the 12th century, and the iron hinges of the later west door appear to be of the same period. 

The chancel was rebuilt on a larger scale early in the 14th century. It is a fine example of 'Decorated' architecture, with a five-light east window and three three-light windows on either side. The priest's doorway, sedilia, and Easter sepulchre are all framed by elaborately crocketed canopies, and the pointing hand carved on the arch of the Easter sepulchre is an unusual feature. The effigy now placed in the sepulchre is not in its original position. There is also a stone credence table projecting from the north wall.

The south aisle and porch were also added during the first half of the 14th century. The former is separated from the nave by an arcade of three arches. The battlemented west tower was built in the 15th century.

Apart from the font and a medieval parish chest the church now contains no ancient fittings, but Rawlinson saw a painting of Christ and the Twelve Apostles on the door that formerly opened into the north transeptal chapel. It bore an inscription commemorating its donor, John Spynell (who is known to have been living in 1458), and his wife Margaret.

John Bushell (vicar 1666–1715) let more light into the interior of the church by removing the door into the north chapel with its 15th-century painting and replacing it by a window. This done, the pulpit and reading-desk were moved into that corner of the building. An inscription formerly on the chancel screen recorded that the church was 'beautified' in 1694. 

The north transeptal chapel had evidently been appropriated to the use of the lords of the manor, for the Rolles family are said to have used it as a burial place from time immemorial. In 1721 the parish at a vestry meeting formally accorded its use to the new lord, Paul Jodrell, and granted him permission to use it as a place of interment and to set up monuments within it. He on his part agreed to keep the chapel in repair for the future and to provide the church with a singers' gallery. 

The fabric was apparently neglected in the mid18th century. In 1759 the archdeacon had to order weeds, nettles, roots, and rubbish to be removed from the church walls, and ivy to be pulled out of the walls of the chancel. The pavement was to be made even in many places. 

At some time before 1822 a new roof was constructed. A drawing by Buckler of that date shows that the roof of the medieval church was once high pitched and had been lowered. The marks of the old roof were then visible on the tower. 

In the 19th century, during the incumbency of the Revd. E. B. Dean (1842–55), the chancel was completely restored at the charge of All Souls College. The restoration was carried out with considerable care in 1845 by an Oxford architect, Johnson. His removal of the Caroline tombs from the east end set free the sedilia and revealed the credence table. On the other hand the tombs themselves are now seen to less advantage in their present position at the west end of the chancel, and they have lost the marble canopies that once surmounted them. The Victorian altar rails may have been substituted at this time for the twisted baluster rails of 1699.

The old pews had been taken out of the nave in 1836 and it had been reseated to accommodate a growing congregation. Still it was reported in 1854 to be in very bad repair. The gallery which Paul Jodrell had erected was now taken down, and in 1863 a complete restoration of the nave and aisle was taken in hand. The work was entrusted to Arthur Blomfield. He removed the flat lead roof which had previously covered the nave and replaced it by a tiled roof of the original pitch. The church was refloored in 1883. The Jodrell chapel was restored in 1914 by Sir Alfred Jodrell. Electric light was installed in 1936. The organ was removed in 1949 from the south aisle to the west end of the church, so allowing the aisle to be refurnished as a chapel as a thank offering for the preservation of the church and parish in the Second World War.

A few small fragments of medieval stained glass have been worked into the heads of the chancel windows, and the old floor-tiles which were once scattered in various parts of the church have been brought together and laid down at the entry to the vestry. One medieval monument remains, the stone effigy of a lady in wimple and long gown, now lying in the chancel. Her arms, a shield semée of crosses patée, two trumpets in bend, if correctly blazoned, point to Trumpington and perhaps show her to be a wife of the John Trompeton, who was one of the jurors of the parish in 1341. On the chancel pavement there once lay the brass of the last rector, John de Aldebourne, who was still living in 1352, a half figure with amice, alb, and an undated inscription. The figure is now affixed to the south wall of the chancel, and a fragment of the inscription is on the north wall.

At least two brasses have disappeared; that which bore the effigies of John Rowsse, husbandman (d. 1485), and his wife, and a brass plate to William Brooke, yeoman (bur. 1587). A fragment of a brass inscription which once marked the grave of Robert Knody (1465–1512) is now fixed to the north wall of the chancel, and there is also a brass inscription to Robert Whitton (d. 1611/12) and his wife Mary. If a wall-painting of the final Doom once occupied the usual position over the chancel arch, it disappeared in 1759 when the walls at the entry to the chancel were ordered to be scraped clean. 

Early in the reign of Charles I the appearance of the east end of the church was altered through the erection of two large tombs, one on either side of the altar. They have recumbent painted effigies and were originally surmounted by canopies on red marble pillars. One that has two children kneeling beneath commemorates William Deane of Nethercote (d. 1620) and his wife Isabel (d. 1624); the other is the tomb of Mrs. Deane's sister, Lady Dorothy Fleetwood (d. 1629), and of her husband Sir Thomas Fleetwood of Missenden (d. 1625). 

In the Jodrell chapel an immense wall monument (unsigned) commemorates the death of Paul Jodrell in 1728. The inscription gives details of his life and enumerates all the members of the Rolles family buried in the church since 1536. Another inscription records that the chapel was repaired by his son Paul Jodrell in 1734. A marble monument by P. Bazzanti of Florence was erected in 1833 to Richard Paul Jodrell (d. 1831). Inscriptions to Sir Richard Paul Jodrell, 2nd Bt. (d. 1861), to the Revd. Sir Edward Repps Jodrell, 3rd Bt. (d. 1882), and to others of the family have been added. There are wall tablets to Elizabeth Jodrell (d. 1794), to Henry Jodrell (d. 1814), and to Lucinda Lady Jodrell (d. 1888) by Gaffin of Regent St., London. There is also a lifesized marble effigy of the Revd. Sir Edward Repps Jodrell (d. 1882) by Sir J. E. Boehm, Bt.

The following memorials are also in the church: a marble wall monument (unsigned) with bust of John Scrope, Secretary of the Treasury (d. 1752); marble tablets to Frances Samwell (d. 1730), daughter and coheiress of Arthur Samwell; Prudence Lenten (d. 1731), widow of Heritage Lenten of Nethercote; Francis Fane (d. 1757), nephew of John Scrope; Mrs. Charlotte Fane (d. 1758), wife of Henry Fane; the Revd. Thomas Skeeler (d. 1763), vicar, and his wife Jane and son Francis; and to Charles Botterell Hawkins, vicar for 40 years (d. 1835). There are brass inscriptions to members of the Fane family of Wormsley: to Maj. John Augustus Fane (d. 1908), Col. John William Fane (d. 1875), John H. Scrope Fane (d. 1928), and to Francis Luther Fane (d. 1954).

There were once memorial inscriptions that have been removed in the course of the various restorations: to John Bushell, vicar (d. 1715); to Heritage Lenten, Esq., of Nethercote (d. 1715); to Francis Bernard (d. 1715), Rector of Brightwell (Berks.), and a number of other inscriptions to children of the Rolles, Croke, and Winlow families. 

Stained glass was placed in the west window of the tower in 1883–7 as a memorial to the Revd. Sir Edward Repps Jodrell, Bt. Two of the chancel windows contain glass in the pre-Raphaelite style dated 1863 and 1868. In 1936 a stained glass window designed by J. C. Powell & Sons, London, was erected in the nave to the memory of the Revd. M. B. Thurburn (vicar 1920–34) and his wife.

The chantry commissioners of 1552 found two chalices without covers. The church now owns an engraved silver chalice and paten cover, both of 1576, and a plain silver paten of 1658. In 1553 there was a ring of four bells and a sanctus bell. Before 1950, when a new treble bell was added, there were five bells, all of them with inscriptions, such as 'Feare God', 'Hope in God', and 'Prayes God'. Two were dated 1636, and the whole ring was by Ellis Knight I. The ancient bells now stand at the west end of the church. There is also a sanctus bell of 1744. 

The registers date from 1666.

Historical information about St. Margaret's Church is provided by 'Parishes: Lewknor', in A History of the County of Oxford: Volume 8, Lewknor and Pyrton Hundreds, ed. Mary D Lobel (London, 1964), pp. 98-115. British History Online http://www.british-history.ac.uk/vch/oxon/vol8/pp98-115 [accessed 22 March 2023].

St. Margaret's Church is a Grade I listed building. For more information about the listing see CHURCH OF ST MARGARET, Lewknor - 1182190 | Historic England.

For more information about St. Margaret's Church see Parishes: Lewknor | British History Online (british-history.ac.uk).