The transformation of Aristotelian natural philosophy and Galenic-Avicennian medicine in sixteenth-century colonial Mexico illustrates how European Scholastic traditions adapted to new environments, epistemologies, and practical needs. At the Royal University of Mexico (founded 1551), the Aristotelian corpus formed the backbone of natural philosophy and medical education. However, university-trained physicians such as Francisco Bravo and Agustín Farfán began to incorporate empirical observations and Indigenous materia medica into their work, blending Scholastic scientia with local practice. Outside the university curriculum, important centers of knowledge production emerged, particularly at the Colegio de Santa Cruz de Tlatelolco, where Indigenous scholars collaborated with missionaries to record botanical and medical knowledge. Works such as the Florentine Codex by Bernardino de Sahagún and the Códice Badiano by Martín de la Cruz and Juan Badiano documented local diseases and treatments based on direct empirical observation and Indigenous epistemologies. This knowledge informed broader intellectual currents to both complement and challenge Scholastic paradigms, as authors such as the Jesuit José de Acosta drew heavily on Indigenous expertise while framing their works within European natural philosophy. My project examines the dynamic exchange between Scholastic Aristotelianism and empirical natural history in colonial Mexico, analyzing how medical and philosophical knowledge circulated between universities, colonial institutions, and Europe. By connecting university practice with natural histories beyond the Aristotelian canon, it sheds light on the global circulation and localization of scientific knowledge.