In 1091, Pierre de l'Étoile founded a Benedictine monastery on the banks of the Creuse, near the spring or "fount" of Gombaud.
In the 15th century, the abbots of Fontgombault had numerous ponds dug, as was also done at the abbeys of Saint-Cyran and Méobecq, thus contributing to fish husbandry in the Brenne region of the Berry province.
It was eventually bought back for religious uses in 1849 by the Trappists, who re-established it as a viable community by redeveloping its agriculture and setting up a kirsch distillery.
In 1948, the empty buildings were restored to the site's original purpose when 22 monks from Solesmes Abbey settled it afresh as a Benedictine community.
In 2013, 13 brothers from Fontgombault transferred to the abbey of Saint-Paul de Wisques in order to strengthen the declining community.