The nave of the church has 4 bays of early 13th-century N arcade with double chamfered round arches. It has circular piers with octagonal, chamfered imposts, and capitals decorated with trumpet scallops with stiff-leaf foliage. However, the tall form of the arcades suggests that a dramatic transformation took place in the 15th or 16th century. Buckler illustrated these arcades in the early 19th century (Vol. VIII, plate 59). In c1300 the west tower was added. The only 12th century fabric surviving is a font bowl.

The manor of Charlton was held at the time of the Domesday Survey by the Church of Malmesbury. There was land for 13 ploughs and a mill rendering 15s. The church was standing at Charlton in the late 12th century and in 1248 it was called a chapel, served by Malmesbury (VCH XIV, 48-50).