It comprises the remains of the preceptory (headquarters) of the Knights Hospitaller of the Order of St John of Jerusalem in Scotland.

Nevertheless, the surviving crossing of the church (below the central tower) retains some of the best-preserved late 12th-early 13th century masonry in Scotland, with refined architectural detail.

It has been suggested that these stones are of much earlier origin than the medieval Preceptory, possibly being related to the important Neolithic henge and burial mound at Cairnpapple Hill, to the east.

The large kirkyard has a fine collection of 17th–18th century headstones, with much intriguing 'folk art', including symbols of mortality, tools representing professions etc.

Torphichen was one of many major Hospitaller sites in Britain, second only to the Priory of Clerkenwell in London, and benefited greatly from this transfer of land.

The Hospitallers fought on the English side during the Wars of Scottish Independence, and withdrew after the Scots victory at Bannockburn, returning during the rule of Robert the Bruce.