A 1596-m-deep borehole (CS–1) located in the central part of the Cínovec (Zinnwald) granite cupola mineralized in Sn and W intersected zinnwaldite granite (ZG) followed by lithian annite (“protolithionite”) granite (PG). These two types of granite are separated by a transition zone (TZ). We studied the chemical composition of major mineral phases (plagioclase, K-feldspar, micas) by EPMA and LA–ICP–MS analyses. The plagioclase composition corresponds to albite (Ab99.6–91.1) containing 0.09 to 0.18 wt.% Rb2O. Albite crystallized from the magma. K-feldspar is perthitic and shows an increase in Rb concentration (up to 0.83 wt.% Rb2O) in the apical part of the cupola. The partition coefficient KD–RbMi–Kfs is constant throughout the cupola, indicating a systematic re-equilibration of these two minerals with fluid. Lithian annite occurs below –735 m. Its F content decreases with depth and from –940.5 m, OH exceeds F. Magnesium and Ti concentrations show a remarkable positive correlation with depth. The TZ and adjacent area are characterized by strong variations in the chemical composition of micas, reflecting the fluctuation of saturation–oversaturation of residual liquid by a F-rich fluid phase. The Rb concentration in zinnwaldite (up to 2 wt.% Rb2O) strongly increases in the apical part of the cupola owing to a significant transfer of volatiles. The chemical composition of mica evolves gradually from the TZ to the apical zone. The discovery of lithian annite included in quartz at –97 m indicates the formation of zinnwaldite by interaction of lithian annite with F-rich fluid. The octahedral site of lithian annite allows the incorporation of Sn, Nb, Ta and W, replacing Ti. Because of the lithian annite → zinnwaldite transformation, these elements with higher ionic charges are expelled from the mica structure, transferred to the fluid phase and concentrated in the apical part of the cupola. The LA–ICP–MS analyses of the micas confirm this process. We envisage the transport of Sn, Nb, Ta and W in the form of fluorides and the precipitation of cassiterite by hydrolysis of SnF4. Tungsten was probably transported as H2WO4, resulting from the reaction of WF6 with H2O. A similar behavior of Nb and Ta is suggested. The hydrolysis of fluorides leads to a strong enrichment of fluid in HF, which induced albite instability and formation of greisens. Calculations show that the amounts of Sn and W released by the transformation lithian annite → zinnwaldite transformation are close to the estimated reserves of these metals within the Cínovec cupola, corroborating the proposed metallogenic model.