St Michael's Church is situated within a large, irregularly-shaped, wooded churchyard, delineated by a stream on its south-west side. The church was known as Llanfihangel Castell Gwallter during the medieval period, when it was a chapelry in the Deanery of Ultra-Aeron. Castell Gwallter (NPRN 92234) is a motte and bailey castle, some 50m to the south-west of the churchyard, and the two may have been contemporary. The church is thought to have always been in the patronage of the Bishop of St Davids. Llanfihangel-Geneu'r-Glyn had become a parish by 1803 and its living was a discharged vicarage. A holy well (NPRN 400452), renowned for its healing properties, is situated close to the east wall of the churchyard. The lychgate (NPRN 419310) within the church's southern boundary is Grade II listed. The church's present bell was hung in 1686.

The form of the medieval church is not known. It was largely rebuilt in the later eighteenth century as a symmetrical cruciform church. There was a gallery with a double staircase leading to it. There was an elaborate, timber, Classical domed cupola above the crossing. The church covered a larger area than that of the present church.

The church was demolished in 1884-1885 and a new church built on the same site and in the same location, but retaining nothing from the earlier fabric. The church was constructed to the designs of A. Ritchie, Chester. It consists of four-bayed nave, two-bayed chancel, south porch and vestry/boilerhouse (south of chancel). The organ chamber was added in 1929.

Sources include:
Cambria Archaeology, 2000, Ceredigion Churches, gazetteer, 48

N Vousden, RCAHMW, 29 July 2014