During the first decade of the nineteenth century, Edinburgh was the scene of several lively debates concerning the structure of the Earth. Though the ideas of groups like the ‘Wernerians’ and the ‘Huttonians’ have received due attention, little has been done to explicate the practice of mineralogy as it existed in the decades before the debates. To dig deeper into the eighteenth-century subject that formed the foundation of nineteenth-century geology in Scotland, this essay concentrates on Rev. Dr John Walker, the University of Edinburgh's Professor of Natural History (1779–1803). In pursuing this topic, it builds on an earlier BJHS article in which I excavated his early career as a mineralogist (1749–79). After first addressing a few historiographical points and the provenance of the student manuscripts upon which this study is based, I explain the method that Walker used to arrange minerals. I then move on to show that, like his younger attempts at mineralogical classification, his mature system was based predominantly upon chemistry. This sets the stage for the last half of the essay where I reconstruct the mineralogical system that Walker taught to the hundreds of students who sat in his natural history lectures from 1782 until 1800. I then conclude with a few observations about the relevance of his mineralogy to the scientific community of late eighteenth-century Edinburgh.