The Dedication is to Thomas a Beckett, Archbishop of Canterbury, who was murdered in 1170. There are, or were formerly, a number of these dedications in the area, others being at Shirenewton, Wolvesnewton, Wyesham, Ganarew and (probably) Penrhos. Such dedications doubtless had a political background reflecting the attitude of the Church in the struggle with the King which had brought about St Thomas's death.

The present church, or part of it, is known to have been in use in 1186 when it was mentioned in the Bull of Pope Urban III. Its original construction can therefore be dated as having taken place in all probability between 1170 and 1186. There may well have been an earlier structure on the site.

Charles Heath, writing in 1800, claimed to identify Saxon features in the arches and windows, but the evidence for this is uncertain.

Some fifty years after being built, in 1233, the church was damaged by fire (as was Monnow Bridge) in the course of the Battle of Monmouth, an action in the baronial uprising against Henry III. In the following year the King authorised the Constable of St Briavels to supply thirteen oaks from the Forest of Dean to repair the damage. In the year 1256 there is an unusual reference to the fact that anchorites were living in St Thomas's.

For the next five hundred years, or more, information about the church is sparse.

In 1479 an Indulgence was granted by the Bishop of Hereford for the repair of the church, but in 1543 John Leland wrote (of the Monnow Gate) "beyond this gate is a suburb in the diocese of Llandaff where once stood the parish church of Saint Thomas, but now only a little chapel dedicated to the saint."

At about this time the Monmouth Cap came into prominence. There is a widespread belief that manufacture of the famous cap was centred in Overmonnow which, as a result, became known as Cappers' Town and Saint Thomas's as Cappers' Church. Mr Kissack however has pointed out (a) that nowhere in the known records is Overmonnow referred to as Cappers' Town, nor is the term used in an contemporary accounts of Monmouth.

In 1611 John Speed published a map of Monmouth, believed to be reasonably accurate, which showed St Thomas's Church with a square castellated tower at the Western end of a small building.

For the next two hundred years or more there is little information to be had. In the general decline in church-going during the period, Monmouth lost four of its mediaeval churches and Saint Thomas's probably came close to suffering the same fate. A contemporary picture shows a scene of neglect and decay. The church was for many years a Chapel of Ease to Saint Mary's Parish Church, and was used for services only on Tuesday.

In 1830 Saint Thomas's again became a separate parish and major restoration of the church was undertaken by Thomas Henry Wyatt, a prolific architect whose uncle was agent to the Duke of Beaufort at Troy House. Wyatt installed new pews and galleries made from oak grown of the Beaufort estates. It has been stated that the galleries came from Raglan Castle which had been dismantled nearly two hundred years earlier at the end of the Parliamentary War, but this is believed to be unlikely. Wyatt rebuilt the West front in brick and added a turret. This turret, depicted in a print of c.1850 has been described as being "curiously slavonic".

Further extensive restoration was carried out in 1874/5 by John Pritchard an architect who had been assistant to the famous Augustus Pugin. Wyatt's turret was replaced and the West doorway reconstructed in stone.

The vestries were added in 1887/8. The present East window dates from 1957.

In 1989-91 an extensive restoration was carried out costing £72,000, under the direction of Jonathan Price, an architect of the firm of Hook Mason of Hereford. The heating system installed in 1966 had its oil-fired boiler replaced by a gas boiler.

Visitation returns of the Archdeacon dated 1846 are in existence (at Dixton) which record that, at Saint Thomas's at that time, one hundred and fifty seats out of a total of four hundred and seventy were appropriated to private use. Further, six seats were classified as first class at £25 each, eight were second class at £20 each, seven third class at £15 each and two fourth class at £10 each. There was presumably a fifth class. The difficulty of accommodating four hundred and seventy persons in the church as we see it is immediately apparent, the figure probably represents an earnest hope rather than a record of fact. The careful division of the congregation into no less than three different categories is interesting and unusual. The categories were presumably based on wealth and social status, and probably reflect the influence of the Duke of Beaufort's agent.

As the church stands at present its most noteworthy feature is the Norman chancel arch, regarded as a fine specimen of its kind. There is a Norman piscina in the South Wall, and the two doorways in the North face have been described as original work. In general the nineteenth century restoration work was carried out with a good deal of sympathy and regard for the character of the church.

Of the two fonts in the church, that on the South wall is unusual. The pillar is covered with basket work decoration and the bowl has faces of a man and woman, together with serpents and birds. It is probably a Garden of Eden scene. Such decoration was popular in the Celtic period, but the font's state of preservation suggests that it is not of great antiquity. There are two carved figures in the church; they were found in recent years in a loft at the church hall, and they were on one of the earlier turrets of the church - their style has something in common with the three heads under the so-called 'Geoffrey's Window' in Priory Street, Monmouth.

Externally there is a Garden of Rest for the interment of created remains. The Calvary Cross in the Garden was restored in 1974. The handsome three storey residence opposite the church is the former vicarage. This was bought in 1864 and sold in 1967 when a new vicarage was built in the grounds.

Within the boundaries of the parish there was formerly the chapel of Saint Duellus, known to have been in existence in the year 1186. It stood above the River Trothy close to the Southern end of the motorway tunnels. Little is known of its history but part of it was still standing in 1956 when it was bulldozed into a nearby well. It now survives only in the names of St Dials Farm and Holywell Wood. This chapel may well have been the source of various articles in the locality whose origin is not known, e.g. one of the fonts in St Thomas's.