The ruins of the church are situated to the E of the town, in the area called the Nungait. Only the nave now survives, but originally the church consisted of a rectangular two-chambered structure, excavations revealing that there was a squared chancel east of the nave. Surviving evidence shows that the nave was vaulted, but it is thought that the vault was added, along with the exterior buttressing, in the 13th century. The side walls of the nave have large, single-splayed, rounded windows without decoration. However, the original chancel arch does survive, as does one voussoir re-used in the N interior wall.

Little is known about the early history of Haddington. The Burgh was founded by King David I and a church dedicated to the Virgin was granted by the king in about 1134 to the church of St Andrews. Then, sometime between 1153 and 1178 Alexander de St Martin was given lands near Haddington by the Countess Ada (widow of Prince Henry, son of King David I); it is not known if this included the present church. In 1178, Ada founded a priory (nunnery) in Haddington and Alexander de St Martin appears to have gifted the lands and buildings of St Martinsgate to this. At a later date, it is known that the nunnery held courts ‘apud Ecclesiam S. Martini in lie Nungait’. In 1567, the prioress disposed of the priory lands, which were then conferred by Queen Mary on William Maitland of Lethington.

There is no agreement for the date of St Martin's Church, with suggestions ranging from the early-12th century through to the late-12th century. The simplicty of the structure leads one to think it is earlier rather than later, but the recorded history leaves it open to the possiblity that the church only came into existence with the foundation of the priory.