It was founded by Saint Bernard of Clairvaux in 1118, only a few years after he left Cîteaux Abbey to found Clairvaux Abbey. Located in a small forested valley 60 kilometres northwest of Dijon, it achieved great prosperity in the twelfth and thirteenth centuries. Fontenay enjoyed the protection of the Kings of France but was plundered in the Hundred Year's War and the Wars of Religion. Later, its fortunes declined, and the refectory was demolished by the monks in 1745. The abbey was closed in the French Revolution, and became a paper mill until 1902, owned for most of its period of operation by the Montgolfier family.
The abbey was bought by Édouard Aynard in 1905 and restored. Apart from the demolished refectory, it retains almost all of its original buildings: church, dormitory, cloister, chapter house, caldarium or "heating room", dovecote and forge, all built in Romanesque style, with later abbot's lodgings and infirmary. Today the abbey buildings are set in modern manicured parterres of lawn and gravel. It is one of the oldest and most complete Cistercian abbeys in Europe, and became a UNESCO World Heritage Site in 1981.
The church of the abbey was built from 1139 to 1147, and was dedicated by Pope Eugene III in 1147. It has a cruciform plan, with a nave 66 metres long and 8 metres wide, with two aisles, and a transept measuring 19 metres. The cloister measures 36×38 metres. The chapterhouse is vaulted, with heavy ribs. The large dormitory is roofed with fifteenth-century chestnut timbers.