The first written mention of the village of Flavigny was in the Latin form of its name, Flaviniacum, which appears in the cartulary (or charter) of the Benedictine abbey founded on the site by a certain Widerard in 719.

In the mid-9th century, in response to the increasing frequency of Viking raids, the relics of Saint Reine (or Santa Regina) were removed from the nearby town of Alise to Flavigny in the hopes that they could be better protected in a more fortified setting.

The town was prosperous during the Middle Ages, catering to large numbers of pilgrims, both those who came to visit the relics of Saint Reine and those on their way to Santiago de Compostela.

The abbey now houses the factory which manufactures Les Anis de Flavigny, small aniseed-flavored pastilles distributed worldwide.

The Benedictine monks there live according to the rule of St. Benedict and offer retreats for lay Catholics and workshops on desk top publishing and the manufacturing of icons.