From the 17th to the 18th centuries, missionaries in Southeast Asia dedicated themselves to providing and establishing a professional medical-pharmaceutical supply for the local population and therefore explored the genuine Materia medica for easily available and affordable remedies, especially medicinal plants. In characteristic medical-pharmaceutical compendia, which can be classified as missionary pharmacopoeias, they laid down their knowledge to advise others and to guarantee a professional health care. As their knowledge often resulted from an exchange with indigenous communities, these compendia provide essential information about traditional plant uses of Southeast Asian people. Individual missionaries such as the Jesuit Georg Joseph Kamel (1661–1706) not only strove to explore medicinal plants but performed botanical studies and even composed comprehensive herbals. The Jesuit missionaries in particular played roles in both the order’s own global network of transfer of medicinal drugs and knowledge about the application, and within the contemporary local and European scientific networks which included, for example, the famous Royal Society of London. The results of their studies were distributed all over the world, were introduced into the practical Materia medica of other regions, and contributed significantly to the academization of knowledge. In our article we will explain the different intentions and methods of exploring, the resulting works and the consequences for the forming of the pharmaceutical and scientific knowledge. Finally, we will show the options which the works of the missionaries can offer for the saving of traditional ethnopharmacological knowledge and for the development of modern phytotherapeutics and pharmaceutical supply. The publication is based on a comprehensive study on the phenomenon of missionary pharmacy which has been published as a book in 2011 (Anagnostou, 2011a) and shows now the potential of historical medical-pharmaceutical works written in the Asian missions of the 17th to 18th century and influenced by ethnopharmaceutical knowledge and the relevance of historical studies for modern investigation in phytotherapy.