What survives of the 12thc. work is the nave of two bays with a W doorway and a S aisle arcade, and the crossing with N and S transepts. In the 1340s, when the 12thc. church was converted into private apartments for the Countess of Pembroke, a floor was inserted just below the level of the crossing capitals and the crossing arches were blocked. At the same time the S aisle wall was removed and a new wall built further S, to convert the area into a guest range with an upper hall. The 12thc. work recorded here consists of the crossing arches, the W doorway, the S nave arcade, the windows of the nave and N transept, and an arch in the E wall of the N transept, presumably leading to a chancel aisle originally. Its counterpart in the S transept is largely obliterated by the insertion of a window during the farmhouse phase of the site's history, but its presence is attested by the N jamb and the outer relieving arch, both visible on the E face.

Benedictine Priory (cell of Ely) (1159–70), Knights Templar preceptory (1170–1308), since 1997 part of the Farmland Museum

Denny was established as a dependent cell of Ely Abbey in 1159, at the instigation of Duke Conan IV of Britanny. In 1170 the Ely Benedictines transferred the cell to the Knights Templar, originally as a preceptory, but by the early 13c it had become a hospital for old and infirm members of the Order. When the Templars were suppressed in 1308 it passed formally to the Hospitallers, who made no use of it. In 1324 it reverted to the Crown. It was formally granted to Aymer de Valence's widow Mary de Valence, Countess of Pembroke, in 1337. Two years later she received a licence to transfer the house of the Franciscan Order of Minoresses (Poor Clares) at Waterbeach to Denny. The Waterbeach site was liable to flooding, but the transfer was not achieved without some opposition. A new church was built to the E of the 12c crossing. At the Dissolution, the Franciscan church was demolished and the remaining buildings were converted for use as a farmhouse. In the early 20c they were acquired by Pembroke College, who placed the site in the guardianship of the Ministry of Works in 1947.

The 12thc. sculptural decoration that survives is mainly distinguished by a wide variety of scallop capital types with plain arches except in the W doorway, which was originally richly decorated with chevron ornament. Directional chevron similar to this, and a variety of related scallop capital forms occur also at Ely Infirmary: unsurprising as this was founded as a cell of the Cathedral priory. It seems clear that the same workshop operated on both sites, and it is just possible that their work at Denny was completed by the time the Templars took over in 1170. It is more normal, however, to date at least the W doorway to the Templar period.