The monastery, dedicated to Saints James and Benedict, was founded in around 739/740 as a Benedictine abbey by members of the Huosi, a Bavarian noble clan, who also provided the three brothers who served one after the other as the first three abbots, traditionally named as Lanfrid, Waldram (or Wulfram), and Eliland, for nearly a century.

Under the influence of Conrad II, Holy Roman Emperor it was rebuilt and in 1031 returned to the Benedictine rule and re-settled by monks from Tegernsee Abbey under the first abbot of the new foundation, Ellinger.

In 1052, Bishop Nitker of Freising, had been granted the abbey by Emperor Henry III without the knowledge of abbot Gothelm.

[6] Gotschalk, now abbot, was responsible for the translation of the relics of Saint Anastasia here in 1053, which by making the abbey a place of pilgrimage added substantially to its fame and prosperity; he was also its first historian.

During the Thirty Years' War the grammar school was suspended and in 1632 Simon Speer was tortured and put to death by the Swedes for refusing to surrender the goods of the abbey.

Johann Michael Fischer built the Anastasia Chapel in the Abbey Church of St. Benedikt (1750–1758), considered a jewel of Baroque architecture[11] In 1684 the Bavarian Congregation of Benedictine monasteries was founded by Pope Innocent XI, to which Benediktbeuern belonged until its dissolution in 1803.

In 1700, Benediktbeuern librarian and archivist Karl Meichelbeck (1669–1734) – people called the monk the "Livy of Bavaria" – used the source-critical method of historiography for the first time in South Germany.

Some of the former monks took posts as university professors: for example, Ägidius Jais went to Salzburg as a pastoral theologian; Sebastian Mall to Landshut as an orientalist; and Florian Meilinger to Munich as a mathematician.

A number of these, and many of the codices, were added to what is now the Bayerische Staatsbibliothek in Munich and the remainder left to be dispersed over time by the neglect or indifference of subsequent owners.

[1] The Meierhof, the old abbey's "steward's house" has been restored to the Centre for Environment and Culture Benediktbeuern with conference rooms and accommodations for guests.

On August 26, 2023, as a result of a storm with hail and heavy rain, all buildings in the complex, including the basilica and Anastasia Chapel, were affected.

The damage to the roof also led to water ingress in connection with its absorption into the historical, wooden building structure, so that some parts are considered to be at risk of collapse.