Left: The chancel, altar, and east window of the church.

After the execution of King Charles I in 1649, Oliver Cromwell's parochial minister for Ilston was John Myles. When the Commonwealth Period ended with the Restoration in 1660, Myles was replaced. Not a man to be easily defeated, John Myles moved further down Ilston Cwm and established the first Baptist chapel in Wales on the site of the abandoned Trinity Well oratory. In 1928, David Lloyd George unveiled a memorial to Myles which can still be seen at the site. With the Restoration of Charles II to the throne, and the implementation of the Conventicle Act in 1664, Baptist services were declared "dissenting assemblies". Myles had no option but to gather up his flock and head for the safety of America. They settled in Massachusetts, at a town they called Swansea.

Until 1974, the tower held three bells. Two were cast locally by David Davies of Oystermouth in 1715, while the third was cast by Jeffries medieval bell foundry at Bristol in the late 15th or early 16th century. The 18th century bells bear the names of the church wardens of the time: Thomas, William, and Richard Bowen. In 1974, the older bell had to be taken down and housed in the nave after a crack appeared in its crown. The defect is thought to have been caused by incorrect hanging or the action of the iron of the 'cast-in' staples in the bell metal. The bell bears the Latin inscription Sancte Thoma Ora Pro Nobis — St Thomas pray for us — a reference to St Thomas à Beckett, a popular saint in the devotional life of worshippers in pre-reformation days. During the Great War of 1914-18, the old bell became known locally as the Angelus, or Peace Bell of Ilston, because the Rev John Veale Roberts (1886-1929) would ring it every day at noon as a sign for his parishioners to offer up prayer to those fighting in France.

The image of St Illtyd (left) was commissioned in memory of, George and Elizabeth Jones of Ilston. The image of Christ's ascension (right) was commissioned by, Elizabeth Jones of Ilston in memory of her parents William and Jane Davies.