The late-12thc church appears to have consisted of an aisleless nave and chancel. It was greatly enlarged in the following centuries. Blocked off on its W side from the present parish church, the original chancel arch survives. The present 18th-c nave is built on top of part of the 12th-c lower courses of the N wall, including the lower courses of the original doorway which led into a cloister. A loose base and some re-used corbels also survive.

In February 1563/4, James Sandilands resigned all property of the Hospitallers in Scotland into the hands of Mary, Queen of Scots, but almost immediately had a regrant of them as a hereditary barony of Torphichen. In the following years, the buildings were allowed to deteriorate, but the nave continued to be used as the parish church. In 1756, the nave was rebuilt. The transepts and tower became a courthouse, but the tower later fell into disrepair and was only finally re-roofed in 1947, twenty years after other restoration work had been carried out by the Ministry of Public Buildings and Works. The Preceptory buildings and ruins came into the care of Historic Scotland, but the parish church remained in use, separated from the transept area by the blocked-off chancel arch.

The first specific reference to Torphichen, the first and only Scottish preceptory of the Knights of St John (Hospitallers), comes c. 1168 in a charter of King Malcolm IV of Scotland. Dugdale and Dodsworth (1661) printed John Stillingflete’s ‘Liber de nominibus Fudatorum Hospitalis S. Johannis Jerusalem in Anglia’ of 1434 in an additional volume to the Monasticon Anglicanum. This document states that King David of Scotland was the person who gave (‘dedit’) land of ‘Torphigan’ to the order. By 1178 the preceptors had presentation to the ‘chapel of Torphichen’. Although it was sited in Scotland, the preceptory of Torphichen was essentially filled with Englishmen and was tied to the main Hospitaller house of St John’s Clerkenwell in London. Willam Wallace occupied Torphichen in the spring of 1298, at which time the brethren may have moved out until later in the year. During the summer of 1298, Edward I, king of England, passed through Torphichen. It appears that it was through Edward’s successes in Scotland that the Hospitallers were able to re-establish themselves there. After the Knights Templar were disbanded in Scotland in 1312, most of their land and possessions came to the Hospitallers. But in 1314, after the Scottish victory at Banockburn, the Knights Hospitaller left Scotland. They returned only after reconciliation with Robert the Bruce. After this, men from Scotland seem to have become the preceptors of Torphichen. From 1471 for six years, there was a campaign to raise money for the preceptory of Torphichen as buildings were said to be partly decayed and ruinous. In 1550 James Sandilands became the last preceptor, a post he held for four years, but in 1554 the order of Knights Hospitaller was suppressed in Scotland.

Waterleaf capitals, water-holding bases and keeled shafts seem to make their first appearance in Scotland at St Andrew's cathedral, begun in 1161. Comparisons with the work there are inevitable, but another church, at Holm Cultram, now in England but founded by Henry, son of King David I of Scotland in 1150 with Cistercian monks from Melrose Abbey, also has a number of similarities, including some waterleaf capitals, the spirals of which continue onto the upper band of the capital. The corbels reused on the S transept and the head on the S exterior wall of the nave are all likely to be of a similar date – either late-12thc or 13thc – and should therefore be associated with either the first stone preceptory church or the first extensions. The larger corbel at the E end of the S exterior wall of the nave may well be later. The surviving carved stonework, comparisons and historical evidence suggest that what remains from the earliest church is likely to date to the last three decades of the 12thc.