The church was restored in 1863, when the Romanesque chancel arch was replaced by the existing one. The N nave doorway (now a window) was also rediscovered at this time. The N chapel, originally built in the 15thc, was rebuilt in 1928. The S porch is of 15th/16thc date. The church appears to have been originally a rectangular nave with a square-ended chancel. There is a W tower, but it is not certain whether this was part of the original plan. The tower appears to have been rebuilt in the 16thc above the first-floor level, but repairs to the tower also took place in 1657 and to the bell-house in 1765.

Mentioned in the Glasgow Inquisition of c. 1120, St Mungo’s church at Stobo was the most important church in the upper Tweed Valley during the early medieval period. Pope Alexander III confirmed the church to the bishop of Glasgow, Engelram, in 1170. This was confirmed several times throughout the rest of the 12thc and early 13thc. Sometime before 1266, and most likely in the early 12thc, Stobo became a prebend of Glasgow Cathedral, which continued as such until the Reformation. The advowson of ‘Stobou’ was confirmed by the pope in 1216, and in 1319 Edward II of England, as Overlord of Scotland, claimed to exercise the right of patronage. ‘Peter, the dean of Stobhou’ witnessed charters of the bishops of Glasgow between 1175 and 1199. In 1369, 1482 and 1486, Stobo appears as one of the baronies of the bishopric of Glasgow, and in 1489-90 it was erected by King James IV of Scotland into a free regality of Robert, bishop of Glasgow, and his successors. Stobo had 5 chaplaincies: Lyne, Broughton, Kingledoors, Dawic and Drummelzier.

Judging from the surviving carved stones, the church appears to date from the 12thc, most likely the first half. The tegulated stone fragment is almost certainly from a coped grave cover and may be of similar date, as suggested by Lang.