A document dated 1146 confirms that Count Adalbero von Froburg was the benefactor of the monastery. This meant that he secured control of the important trade route across the Hauenstein. The monastery church was consecrated in 1187 and dedicated to the Virgin Mary. The first mention of Benedictine nuns was in 1266. Around 1400, when the Froburg line died out, the district of Waldenburg came under the jurisdiction of the city of Basel. Shortly afterwards, the Servite Order took over the monastery.  On the anniversary of the consecration in 1525, four years before the Reformation in Basel, the tenant peasants plundered and vandalized the monastery. As of 1541, the Bürgerspital in Basel city received the revenues from the dairy farm on the monastery’s land, designated in part for the care of the poor and the sick.

A brickworks was operated in the monastery church between 1645 and 1682. To this very day, the church and monastery building are still clad in those bricks. After the separation of Basel into two cantons, the Basel banker Merian purchased the monastery in 1833 as a summer retreat for his family – the nearby village of Langenbruck was developing into an aspiring resort. Meanwhile, the leaseholders of the estate used the church to store tools and wood. In 1967 the canton Basel-Landschaft listed the church as a monument. However it was left to the later founder of the Schoenthal Monastery Foundation to undertake its renovation and to establish the site as a place of art in 2000. In 2018, the foundation Sculpture at Schoenthal merged with the Edith Maryon Foundation. The artistic and cultural programme will be continued by the "Verein Kloster Schönthal".