In colonial Spanish America, missionaries served as important collectors and mediators of indigenous knowledge of the natural world. Missionaries, especially Jesuit missionaries, provided some of the earliest accounts of American nature. Much of this knowledge came from their contacts in indigenous communities and, as a result, missionaries played a vital role in the assimilation of indigenous knowledge to European ways of understanding the natural world. Focusing on missionary accounts of indigenous knowledge of medicinal plants, this paper will explore the role of Jesuit missionaries in the secularization of indigenous knowledge – a process whereby missionaries stripped away any spiritual meaning that local nature had according to indigenous worldviews and religions. Instead, many missionaries reported and encouraged others to report only the pragmatic use and empirical information about natural phenomena. What is interesting is that the Jesuits and other missionaries had religious motivations for engaging in the secularization of indigenous knowledge of nature, especially in seventeenth-century Peru during the campaigns to extirpate “idolatry” among native Andeans. Consequently, this paper seeks to highlight the role that Jesuit missionaries played in making New World nature knowable to European sciences, while also emphasizing their underappreciated role in the secularization of indigenous knowledge – a process that has echoes in the persistent tendency to characterize indigenous informants as purveyors of empirical observations.