The Templars built a number of additions, including a large Norman-style arched doorway and a refectory. Denny became a hospital for sick members of the Order in the mid-13th century. By the end of that century, the Knights had lost their power, and in 1308 King Edward II had all the members of the Order arrested and imprisoned for alleged heresy, confiscating their property. Denny was then given to the Knights Hospitaller, who took no active interest in the property. In 1324 it was taken back by the Crown.
In 1327 King Edward III gave the Priory to a young widow, Marie de Châtillon, Countess of Pembroke, known for her founding of Pembroke College, Cambridge. Countess Marie turned what had been the Abbey church into her lodgings. She had a new church built and gave the remainder of the priory to the Franciscan Poor Clares. This community of nuns moved from their flood-prone Waterbeach Abbey. The priory was expanded in this period, with comfortable quarters for the Countess, who never entered the Poor Clares, and spartan accommodation for the nuns. The priory began to be called Denny Abbey during this period, despite the fact that the term "abbey" is never used by the nuns of that Order. The Countess of Pembroke died in 1377 and was buried before the high altar of the nuns' church in Denny Abbey, but the precise location of her grave is now lost.
Katherine de Bolewyk, first abbess 1342, occurs 1351
Margaret, occurs 1361
Joan Colcestre, occurs 1379
Isabel Kendale, occurs 1391, 1404
Agnes Massingham, elected 1412
Agnes Bernard, occurs 1413
Margery Milley, occurs 1419, 1430-1
Katherine Sybyle, occurs 1434, 1449
Joan Keteryche, occurs 1459, 1462, died 1479
Margaret Assheby, occurs 1480, 1487, 1493
Elizabeth Throckmorton, occurs 1512, last abbess. She took with her when she left the wooden dole-gate of Denny Abbey, carved with her name, which can still be seen at Coughton Court.
The abbey was closed in 1536, during the Dissolution of the Monasteries, and was once more taken over by the Crown. The last of the nuns had left within two years. The Abbess's lodge, originally built for the Countess, was retained as a farmhouse, and the Refectory as a barn, but the nave was demolished. In 1628 the abbey passed into private ownership. The barrister John George Witt was born at Denny Abbey in 1836. Pembroke College, Cambridge, which had also been founded by the Countess of Pembroke in 1347, bought the site in 1928. The Abbey, Nuns' Refectory and surrounding land remained a farm until they were leased in 1947 to the Ministry of Works, which later transferred them to English Heritage. The abbey, partially restored in the 1960s, is open to the public alongside the Farmland Museum, who manage the Abbey on behalf of English Heritage. The Farmland Museum, which opened in 1997, has a shop, café and an education centre, running courses for local schools. Farm buildings including the 17th-century barn have been converted into displays of local history and farming, including a 1940s farm labourer's cottage, a 1930s village shop, displays on local crafts and skills. Many of the old farm tools and machinery came from a museum at nearby Haddenham which closed. It was at Haddenham where interviews were made in the 1970s with local farming people, recording their stories dating back to the beginning of the 20th century. The whole site, known as Farmland Museum and Denny Abbey, is open from April to October, and there are regular special event days. Note: The spellings Denny and Denney appear with equal frequency in the historical literature. The latter spelling is no longer used locally, in modern times.