This article offers a discussion of Duhemian analysis of Newton's method in the Principia considering both the traditional response to this analysis and the more recent ones. It is argued that in General Scholium to the Principia, Newton is not advocating what Duhem suggests in his best-known criticism, but he is proposing something very close to the establishment of a logical priority of physics over metaphysics, a familiar thesis defended by the French physicist himself.