Elucidation of time-space relationships between a given wolframite deposit and the associated granites, the nature of the latter, and their alterations, is a prerequisite to establishing a genetic model. In the case of the world-class Panasqueira deposit, the problem is complicated because the associated granites are concealed and until now poorly known. The study of samples from a recent drill hole and a new gallery allowed a new approach of the Panasqueira granite system. Detailed petrographic, mineralogical, and geochemical studies were conducted, involving bulk major and trace analyses, BSE and CL imaging, EPMA, and SEM-EDS analyses of minerals. The apical part of the Pansqueira pluton consisted of a layered sequence of separate granite pulses, strongly affected by polyphase alteration. The use of pertinent geochemical diagrams (major and trace elements) facilitated the discrimination of magmatic and alteration trends. The studied samples were representative of a magmatic suite of the high-phosphorus peraluminous rare-metal granite type. The less fractionated members were porphyritic protolithionite granites (G1), the more evolved member was an albite-Li-muscovite rare metal granite (G4). Granites showed three types of alteration processes. Early muscovitisation (Ms0) affected the protolithionite in G1. Intense silicification affected the upper G4 cupola. Late muscovitisation (Fe–Li–Ms1) was pervasive in all facies, more intense in the G4 cupola, where quartz replacement yielded quartz-muscovite (pseudo-greisen) and muscovite only (episyenite) rocks. These alterations were prone to yield rare metals to the coeval quartz-wolframite veins.