The church is composed of an aisless nave and narrower, rectangular chancel. The carved medieval-type detailing is mostly (possibly all) neo-Romanesque, the result of a reconstruction of the church in 1846-7 by George Pickering. Sited in the South Bailey, the church sits just outside the SE corner of the priory walls. It appears always to have been a parish church for the use of those living in the south bailey, owned by neither the priory nor the cathedral. Numerous repairs to the church are recorded in the 18thc. and early 19thc. In 1780 an estimate and proposed elevation drawing were made for rebuilding the church. This proposal, however, was never carried further (Durham County Archives, no. EP/Du. ML 9). In 1919, St Mary-the-Less became the chapel for St John's College, University of Durham. The carved stones, formerly loose behind the church and presently inside the church, are recorded to have been in the church cemetery in 1892 (Boyle, p. 377). The church lies E-W but is not quite at the same orientation as the cathedral. It is sited on the N side of the South Bailey Road, the road beginning at the priory gate (now called the College Gate) and continuing to the S end of the peninsula, where the present Bailey Gate (known as the Watergate) is sited. From here it leads down a path to Prebend's Bridge where nearby, in the medieval period, there seems to have been a ford across the River Wear.

Domesday Book does not cover this area.No documents are known to survive concerning the 12thc. origins of the church. St Mary-the-Less was built for the parish of the South Bailey, as opposed to St Mary-le-Bow, which was for the parish of the North Bailey. Surviving references that mention the South Bailey are to be found from the first half of the 13thc. onwards. Throughout the medieval period the church was generally referred to as St Mary in the South Bailey (ecclesiae Beatae Mariae in Ballio Australi) and only at some date after the Reformation was it called St Mary-the-Less or Little St Mary. The earliest surviving definitive reference to the church is in the first half of the 13thc. The first known rector, called 'Ricardus', is mentioned in 1300. Hutchinson suggests that the church advowson may have first been in the hands of Bertram Bulmer (d. 1165/6, lord of Brancepeth). Bertram is referred to as a baron of the bishopric in an attack on William Cumin's nephew and adherents in 1144. On the death of his son William in 1176/77, Bertram's daughter Emma inherited the estates. She had previously married Geoffrey Neville, through which the church of St Mary in the South Bailey may have come into the hands of the Nevilles. In 1425, on the death of Ralph Neville, Earl of Westmorland, the inquisition post mortem states that the advowson of the church had been in his possession. In the Papal Taxatio of 1291-2, St Mary-the-less is listed as exempt from taxation.

Stylistical comparisons, along with historical evidence, make it likely that the loose, carved stones date from either the 2nd or 3rd quarters of the 12thc. The voussoir stones compare favorably with the chevron mouldings with soffit chip carvings on the Durham castle gateway entrance arch, though they are not identical. Comparisons with the south doorway in the 2nd bay of the nave of Dunfermline Abbey, a building strongly influenced by Durham Cathedral, are also relevant, as the doorway there may date to around 1140 (a dedication took place in 1150, by which time it is normally assumed that the nave had been finished).

Some drawings/prints show the exterior church of St Mary the Less before the church was rebuilt in 1846-7. Although these show slight differences, they indicate the same basic features: a rectangular nave with arched windows, bell turret above the west end and a south porch (deeper than at present). The chancel, also rectangular, is shown with at least one arched window on the south wall. The depictions differ in certain features. It was George Pickering, clerk of works at Durham Cathedral, who designed the present church of St Mary the Less, as well as several other buildings in the diocese. The nave doorways constructed at St Mary the Less (Durham), St John the Evangelist (Kirk Merrington) and St Bartholomew's (Sunderland Bridge) show his fondness for neo-Romanesque and display similarities in their general design.

In 1844, before the church was rebuilt, R. Surtees described the chancel arch as 'early Norman'. This, along with the mention in the late 19thc. of the carved stones being loose in the cemetery of St Mary's, suggests that they come from the 12thc. church formerly there. No specific references to these stones are known to survive from the period when the church was rebuilt. A likely location would seem to be an interior arch as the carving on both the sides of the voussoirs and the soffits would be difficult to place elsewhere, especially as images of the outer arch of the former church porch arch show no carved decoration, and there are no references to any decorated doorways in the earlier church building. As there appears never to have been a west tower, and therefore no tower arch, this leaves the chancel arch as the most likely source for the now loose, carved voussoirs. The diameter of the half-roll of the stone with a carved roll but no chevron, along the widths of the soffits of the chevron stones suggest that all of the surviving stones come from the same arch, the stone with half-roll being part of one of the jambs.

Suggestions for the date of construction of the church and the person(s) responsible have been made by several authorities. The advowson may have come into the hands of the the Neville family via a marriage between Geoffrey Neville and Emma Bulmer, daughter of Bertram Bulmer. This has been used to support the theory that Bertram Bulmer was the first to hold that advowson. Although this is plausible, it remains only an hypothesis, as is the suggestion that the date of construction was in/around 1140 (some writers now misleadingly stating this as fact). William Cumin established himself in the castle immediately after Bishop Geoffrey Rufus died and claimed the right to become bishop of Durham. Bishop Geoffrey's death is recorded inconsistently in different sources. It was either May 1140 or May 1141, most likely the latter. The date of Geoffrey's death is significant for the possible date of construction of St Mary the Less as it might question the plausibilty of Bertram being allowed to build a church for soldiers in the bishop's bailey during Cumin's control of Durham. Although he had the support of several barons, the king of Scotland and ultimately Empress Matilda (daughter of King Henry I of England), Cumin failed to be consecrated as bishop. Fighting and discord filled the years until he formally left the castle and diocese in 1144. It is unknown where Bertram Bulmer placed his allegiances when Cumin first advanced his cause, but Bertram is mentioned as part of a three-man faction leading troops against Cumin's forces at Merrington in August 1144. The three, stated to have been barons of the bishop, were Roger de Conyers, Geoffrey Escolland and Bertram de Bulmer (Arnold, p.158). An earlier mandate by Henry I to W. Espec and his custodians of the see of Durham, sometime between 1129 and 1133, states that 'Roger de Conyers was to have his ward (custodiam suam) from the knights who do castle-ward at Durham...' (Johnson and Cronne, p. 274 no. 1825 and fn.). It appears that the see of Durham was in the hands of custodians during this period. These included Geoffrey Escolland (Arnold, p. 241, and Johnson and Cronne, p. 231 no. 1604 fn.). Documents state that Roger de Conyers was never in favour of William Cumin, but no specific comment on this is made for either Escolland or Bulmer.

Bishop Hugh de Puiset is recorded as having newly built the wall south to the water gate ('Murum quoque a porta aquilonari usque ad australem novum fecit'). The water gate was the gate at the south end of the south bailey. The reference by Geoffrey of Coldingham (late-12thc. or early-13thc.) may be the first surviving mention of it (Raine, p. 12). Hutchinson (p. 363) writes that prior to Robert Rodes annexing the Water Gate in 1449, the gate had been used for 'the bishop's liege people [who] were decreed to have the privilege of passing that way to and from the shrine of St Cuthbert'.

Bertram de Bulmer is recorded as the son and heir of Anschetil de Bulmer (Bulmere), who had been reeve and later sheriff in Yorkshire. Anschetil died about 1129 and Bertram first appears in the records about 1128-30 as sheriff of Yorkshire (Johnson and Cronne, p. 242, no. 1662 fn.). A Bertram vicecomite also appears as a witness to a grant of the Bishop of Durham. Snape identifies this reference with Bertram de Bulmer. Snape further states that Bertram ceased to be sheriff of Yorkshire in 1163 (pp. 100-1 no. 118). Reginald of Durham mentions Bertram de Bulmer in his Life of Saint Godric in a narrative about one of Bertram's clerics having transferred to knightly service (Coombe, pp. 388-9 no. 214). Bertram died about 1165-6 and was succeeded by his son William, of whom little is known. On William's death in 1175/6, Bertram's daughter Emma succeeded. Emma had meanwhile married Geoffrey de Nevill. Sometime between 1241 and 1249, their son-in-law, Robert son of Meldred, gave land next to the church of St Mary in the South Bailey to the prior and monks of Durham (‘ex don domino Roberti filly Meldredi in ballio Dunelm iuxta ecclesiam beate Marie versus austrum’) (Hoskin, pp. 2-3). Robert also held land in Brancepeth, a few miles SW of Durham, in the same parish where Bertram de Bulmer is thought to have established a castle or manor house (Littledale, p. 214).

The south bailey was inhabited by those who served the priory and the bishop, some of whom were soldiers. Whether the initial intention was to create an area specifically for the castle wardens is uncertain, and other, non-military persons, are recorded as living in that parish in later records (Feodarium). Gerard the Marshall (Gerardus maracallus) sold a piece of land next to the infirmary facing the priory gate to Richard the engineer (Ricardo ingeniatori) sometime between 1170 and 1174, land which appears to have been in the South Bailey (Snape, pp. 104-5 no. 124 and source note). The reference to the infirmary facing the gate confirms that its earliest construction on the site had already taken place by this date. The land was re-sold shortly afterwards to the monks of Durham for making a hospital (Snape, p. 32 no. 36). This infirmary outside the priory gate is recorded, at a later date, as being sited either between the north and south baileys or as part of the south bailey during the medieval period (Surtees Society, Rites of Durham, 1903, pp. 91-2, 105 no. LV, and 273). The Rectors of St Mary the Less appear also to have held properties in the parish (R. Surtees, p. 44 fn.). In the later medieval period, there are references to both men and women making payments ('corrody') that allowed them to move into either the Infirmary outside the abbey gate or the Maison Dieu, the latter apparently in the north bailey (Registrum Parvum III, Durham Cathedral Archive, GB-0033-DCD-REG.Parv.3).

One window, at the W end of the S chancel wall was reportedly moved to that location from the W wall (VCH, p. 138). This and parts of the chancel arch are said to be original, but close examination shows both to be built entirely of 19thc. stone. It is more difficult to ascertain whether any of the stones used on the jambs of the interior side of the present S doorway of the nave are of 12thc. date. The chancel arch has no features that relate to the carving on the loose, carved stones.

A 12thc. reference by Reginald of Durham to a church of St Mary inside the city walls of Durham ('ecclesiam Sanctae Mariae, quae infra urbis maenia sita est') appears in the Libellus de Vita et Miraculis S. Godrici, Heremitae de Finchale. Stevenson (1847, p. 59 fn. 6) suggests that this refers to either St Mary-le-Bow or St Mary in the South Bailey. Boyle (1892, p. 402) proposed that it possibly refers to St Mary in the South Bailey. More recently, Coombe (2022, p. 113 fn. 216) suggests that the reference is more likely to be for St Mary-le-Bow in the North Bailey. A list of rectors given by R. Surtees (p. 41), and copied by few others, includes the name of Thomas in 1241. Later lists do not include this name since Thomas was rector at St Mary-le-Bow, and not St Mary-the-Less.