The Neves Corvo Cu-Zn-Pb(-Sn) deposit (Portugal) is one of the largest volcanogenic massive sulfide deposits (VMS) worldwide, hosted by Upper Devonian to Early Carboniferous rocks. Originally, it contained an early structurally controlled tin orebody (stockwork and massive cassiterite), which has now been mined out. In this study, we report the first occurrence of phosphate minerals (apatite, florencite, and xenotime) within the tin stockwork at Neves Corvo. We present a high-resolution multi-analytical study using petrographic, mineral chemistry, and whole-rock geochemical methods to understand the genesis of these phosphates and their implications for tin at the Neves Corvo deposit. Our results demonstrate that apatite forms coevally with cassiterite and has low trace element contents except for S, Sr, Y, and MREE (Middle Rare Earth Elements; 10–100 ppm) with a bell-shaped chondrite (C1) normalized REE pattern. We suggest that apatite likely formed as chlorapatite or oxyapatite that was subsequently metasomatized to fluorapatite with minor carbonate during hydrothermal alteration related to sulfide mineralization. The REE pattern of apatite, together with the presence of secondary phosphates (florencite and xenotime), indicates preferential scavenging of REE to form the latter phases due to the interaction with NaCl-rich and, to a minor extent, fluorine-rich fluids in an aluminum-saturated system. This study underscores how the analyses of primary and secondary phosphate minerals can help to track the evolution of the hydrothermal system and partially constrain the fluid composition and fluid-rock interaction processes. Therefore, the approaches outlined here are applicable to any hydrothermal ore-forming system where phosphate phases are formed.