The Benedictine monks who opened Denny Priory in 1159 stayed for ten years before returning to Ely, leaving the site to the Knights Templar. The Templars built substantial additions — a Norman-style arched doorway, a refectory — and Denny became a hospital for sick members of their Order in the mid-thirteenth century. By the end of that century the Templars had lost their power across Europe. In 1308, King Edward II had all members of the Order arrested and imprisoned for alleged heresy, their property confiscated. Denny passed to the Knights Hospitaller, who showed little interest in it. By 1324 the Crown had taken it back. What remained was a complex of buildings occupied by three different religious orders across 165 years, each leaving their mark on the fabric of the place.

In 1327, King Edward III gave the priory to a young widow: Marie de St Pol, Countess of Pembroke, who was 24 years old and would live to 74. She is remembered today primarily as the founder of Pembroke College, Cambridge, which she established in 1347. But Denny was her private project, a place where she exercised unusual and personal authority. Countess Marie turned what had been the old Abbey church into her own private lodgings. She had a new church built. She brought in a community of Franciscan Poor Clares — nuns who had been displaced from flood-prone Waterbeach Abbey — and gave them the remainder of the priory. The priory began to be called Denny Abbey during this period, a name that has stuck despite the fact that the Poor Clares technically never called their communities abbeys. Countess Marie died in 1377, was buried before the high altar of the nuns' church, and the precise location of her grave is now lost.

The priory was closed in 1536 during the Dissolution of the Monasteries. The last abbess, Elizabeth Throckmorton, retired to live with her nephew George Throckmorton at Coughton Court in Warwickshire. She took something with her: the wooden dole-gate of Denny Abbey, carved with her name. It can still be seen at Coughton Court today. The other nuns had all left within two years. The Abbess's lodge — originally built for the Countess — was retained as a farmhouse. The refectory became a barn. The nave was demolished. In 1628 the abbey passed into private ownership, used as a working farm for the next three centuries.

Today Denny Abbey is managed by the Farmland Museum, which opened here in 1997 alongside the English Heritage-administered abbey buildings. Farm buildings including the seventeenth-century barn — itself built from stone taken from the dissolved abbey — have been converted into displays of local history: a 1940s farm labourer's cottage, a 1930s village shop, demonstrations of local crafts. The site is open from April to October. The abbey church and refectory buildings survive as Grade I listed structures. The Norman arched doorway the Templars built stands inside what is now a farmyard. The whole complex sits on an ancient road between Cambridge and Ely, on ground that was already old when the Domesday Book named it.