The church was built in the early 12th century on the site of an earlier building, possibly the ancient chapel of St Aaron that was known to have existed as a private chapel for the nearby Llantarnam Abbey.

In the 15th century significant alterations were made to the church and major reconstruction commenced, with the eastern wing renovated.

[1] The tower is of the Tudor architectural style, built of two stages in local stone, and the chancel arcade and stone arches in the early Renaissance shape appear to have been added in the early 16th century.

[1][2] In the 16th century, the poet Sawnder Sion, also known as the "Lion of Llantarnam", of Llantarnam Abbey was buried beneath the choir in the church,[3] witnessed by Dafydd Benwyn, another poet and friend of Sion who wrote a poem mentioning the bed "In the choir of St Michael".

[1] During the "Popish Plot", on Sunday 17 November 1678, John Arnold of Monmouthshire captured Father David Lewis, also known as Charles Baker, at St Michael's Church where he was preaching; he was later executed.