There have been numerous changes to the church. Repairs were undertaken in 1616, but in 1754 the chancel was shortened. Then, in 1774, after the collapse of the W gable, the nave was shortened. In 1784 further work on the church was carried out and still more in 1813. New windows and a new porch were constructed in 1857-8, at which time, the medieval tympanum was moved from its position over the S nave doorway to the outer arch of the new porch. Finally, in 1910-12 the chancel was rebuilt and other work carried out.

Blahan, Presbyter of ‘Lintun' (which is assumed to refer to Linton in Roxburghshire) was present at a meeting of clergy from England and Scotland in 1127. A specific record of the church appears about 1160 with mention of Edward parson of the church of ‘Lintun’. References to Linton continued to occur in charters thereafter. William of Somerville seems to have gone to Scotland with King David I. His son, also called William, witnessed charters of Kings Malcolm IV and William the Lion. William Somerville was supposedly given the Linton lands in 1174 by the latter. In 1214, Roger Somerville died and is said to have been buried in the church. Following this, and for the following two centuries, other members of the Somerville family were buried there. In 1424/26 Thomas, 1st Lord Somerville, had the E division of the church rebuilt. There was also a castle at Linton owned by the Somervilles, which was in existence at least as early as the 13thc and repaired in 1426. The fortress was destroyed by the Earl of Surrey in 1523 at the English invasion of Scotland. It appears that in the later 15thc, the Somervilles sold the property at Linton to the Ker family.

Linton's Church is the only church in Scotland to have a tympanum carved with figural work. Tympana are rare in Scotland, but a few examples do survive, such as that at Abercorn which is carved with a pattern of lozenges. While it has been commonly said that the depiction on the tympanum represents William of Somerville killing a worm that plagued the area, it is more likely that it actually shows either St George or St Michael. There is no known exact parallel for the two beasts, but the bird and figure with lance astride a horse can be compared with representations within the Hereford School of Sculpture, as on a tympanum in the church at Brinsop, which has been compared to sculpted representations in Western France. The baptismal font was apparently formerly used in a Blacksmith's shop, which explains the damaged areas. The grave cover was found outside the church and was cleaned and brought into the church.