Cîteaux was founded in the Netherlands at the end of the 1940s as a result of the intersection of two projects: first, the intention to produce a general history of monasticism in the Netherlands; and second, the creation of a «Commission d'Histoire de l'Ordre de Cîteaux» (Commission on the History of the Cistercian Order) by the Cistercian Order of the Strict Observance at the General Chapter of 1947. Both projects envisaged the production of comprehensive works, and both were forced to limit their ambitions. 

The team of researchers which had been drawn together for the project remained active, however, and in 1947 an internal newsletter was created, entitled Cîteaux in de Nederlanden. This team of historians was then given a more permanent foundation by the creation of o board which met regularly and established annual themes for research. In 1951, under the inspiration of Father Roger de Ganck of Westmalle Abbey and Father Edmond Mikkers of Achel Abbey, this mimeographed newsletter was transformed into a printed journal. In 1959, under the title Cîteaux: commentarii cistercienses, it opened to wider horizons by including articles in French, English, and German as well as Dutch. 

In subsequent years, the journal developed in accordance with the view of its editor, Fr Edmond Mikkers, who died in 1993.

During these years, Cîteaux gained an international reputation et came to be recognised in scholarly circles for the quality of its research.

In 1986, a new editor-in-chief, Brother Jean-François Holthof of Cîteaux Abbey, took over direction of the journal, and he - together with an editorial board of historians, both lay and monastic - further extended the scholarly and historical scope of the journal.

From 1993 Cîteaux has been directed by its editor-in-chief, Dr Terryl N. Kinder, together with an editorial board.