In the Tres Arroyos granite-pegmatite system (Badajoz, Spain) a zoned aplite-pegmatite field occurs, with poorly evolved, intermediate, and Li-rich dikes intruded into metasediments, close to the contact with the Nisa-Alburquerque granitic batholith. A large variety of Fe-Mn phosphate minerals occur in the poorly evolved aplite-pegmatites; Al-phosphates occur mainly in the intermediate and Li-rich dikes. The Fe/(Fe + Mn) ratio of the Fe-Mn phosphates is the highest reported for aplite-pegmatite fields in the Central Iberian Zone, suggesting a low degree of fractionation for the poorly evolved aplite-pegmatites that host these minerals. In contrast, the high F contents observed in crystals of the amblygonite–montebrasite series from the intermediate and Li-rich aplite-pegmatites indicates a higher fractionation degree for these dikes. The relatively common occurrence of phosphate minerals in the three types of aplite-pegmatites from Tres Arroyos attests to a significant availability of P in the pegmatitic melt. In this granite pegmatite system, P first started behaving as a compatible element, thus favoring the crystallization of discrete phosphates, during the crystallization of the poorly evolved aplite-pegmatites. In more fractionated melts, where Fe-Mn-(Mg) contents were extremely depleted, P was still available, allowing the crystallization of the Al-phosphates, mainly of the amblygonite–montebrasite series, in the more evolved intermediate and Li-rich aplite-pegmatites. Subsolidus replacement of the early phosphate phases, such as those of the amblygonite–montebrasite series, by lacroixite, together with the presence of late Ca- and Sr-bearing phosphates such as jahnsite-(CaMnFe), whiteite-(CaFeMg), mitridatite, and goyazite, attest to a high activity of metasomatic fluids in the Tres Arroyos granite-pegmatite system. Consequently, variations in the phosphate mineral associations and in their chemical compositions reflect well the fractional crystallization processes suffered by the pegmatitic melts from the poorly evolved up to the Li-rich dikes, as well as the subsolidus history of the Tres Arroyos system.