The W-Sn Panasqueira ore deposit is a magmatic-hydrothermal system, which includes a high grade quartz-vein type mineralization and underneath disseminated greisen-type mineralization located in the upper part of a two-mica granite. We investigate genetic and chronological relationships between greisenization of the Panasqueira granite and the formation of ore-bearing quartz veins by monitoring major and trace elements variations in quartz-muscovite assemblages composing the two-mica granite, greisen and ore-bearing quartz veins. Greisen is marked by an overall depletion in Mg, Ti, Ca, Na, Ba, Sr, REE and enrichment in Fe, Li, Rb, Cs, Sn, W that reflect the breakdown of feldspars and biotite and implication of W-Sn-bearing fluids during greisenization. Muscovite from greisen and mineralized quartz veins are enriched in granophile elements (F, Rb, Cs, Li, Sn, W and Zn) compared to magmatic muscovite from the two-mica granite. Trace elements contents in quartz depict evolutionary trends with progressive enrichment in Ge and B and depletion in Al, Ti and Li between magmatic and hydrothermal quartz that emphasize the progressive evolution and cooling of the magmatic-hydrothermal system of Panasqueira. Multivariate statistical approach applied on quartz and muscovite data demonstrates similarities in composition between quartz and muscovite from greisen with those composing ore-bearing quartz veins. These similarities suggest that greisenization and the formation of mineralized veins result from the same hydrothermal event and derived from the same source of hydrothermal fluids. Apatite from greisen and quartz vein yielded respectively U-Pb ages of 292 ± 10 Ma and 295 ± 5 Ma confirming that greisenization and the formation of mineralized veins occurred roughly at the same time. These ages also overlap with the cooling age of the Panasqueira granite (296 ± 4 Ma), indicating a temporal and genetic link between greisenization, W-Sn mineralization and the granite crystallization. Temperatures of the magmatic-hydrothermal system constrained by Ti-in quartz thermometry depicts a cooling trend from magmatic quartz of granite (700-600°C) to hydrothermal quartz of greisen (500-400°C) and veins (450-350°C). These results provide evidences that greisenization and the formation of W-Sn bearing quartz veins occurred at the magmatichydrothermal transition, during which orthomagmatic fluids rich in volatils, incompatible elements and metals (W and Sn) were exsolved at the final stage of solidification of the Panasqueira two-mica granite.