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The Fregeneda-Almendra pegmatite field of the Iberian Massif represents a typical expression of peraluminous rare-metal magmatism that occurred over western Europe at the end of the Variscan orogeny. It is the host for two main types of Li-mineralized intrusions, identified at the scale of the Variscan belt, including petalite- or spodumene-rich pegmatites, as well as Li-mica-rich pegmatites, for which the origin of mineralogical-chemical differences is not yet understood. Here, we provide cassiterite and columbite-group mineral (CGM) U-Pb ages along with oxide, mica and phosphate mineral compositions for Li-pegmatites from the Fregeneda-Almendra field in order to assess their petrogenesis and tectonic-magmatic context of emplacement. U-Pb geochronology indicates that petalite-rich and Li-mica-rich pegmatites were mostly emplaced sub-synchronously from 315 ± 6 to 308 ± 6 Ma, during strike-slip deformation and granitic magmatism within an anatectic dome bounding the pegmatite field. U-Pb data and pegmatite geographic zonation suggest that Li-pegmatites were sourced from buried equivalents of leucogranites and migmatites from the dome. Li-pegmatites experienced a complex crystallization including K-feldspar, petalite, topaz, Nb-Ta-Fe-Mn-rich cassiterite, amblygonite-group minerals (AGM) and CGM as early magmatic phases, followed by lepidolite for Li-mica-rich pegmatites. At the magmatic-hydrothermal transition, notably leading to the formation of Nb-Ta-Mn-Fe-poor cassiterite hosting CGM inclusions, earlier minerals were resorbed by muscovite and albite. A later F-rich hydrothermalism is locally reflected by zinnwaldite overgrowths on muscovite. Cassiterite, CGM and micas from petalite-rich pegmatites show lower Mn/Fe ratios and higher Ti contents, along with lower Zr-Ga contents for cassiterite, than that from Li-mica-rich pegmatites. Such behavior is consistent with a magmatic differentiation process whereby Ti content decreased and the degree of Mn-Fe geochemical fractionation and solubilities of Ga and Zr increased in the melts, possibly in relation with high fluorine activity. In Li-mica-rich pegmatites, AGM equilibrated with a melt with up to 2 wt% F, similar to that in equilibrium with lepidolite (1–3 wt%). In petalite-rich pegmatites, the relatively high F concentration of the melts equilibrated with AGM (≤ 1.5 wt% F) contrasts with the liquid equilibrated with muscovite (< 0.5 wt% F). This can be accounted for by muscovite crystallization after the exsolution of a F-rich aqueous phase at the magmatic-hydrothermal transition. Relatively similar F contents in the initial melts of petalite- and Li-mica-rich pegmatites support the hypothesis that the stability of lepidolite does not only involve high F but also a low H2O/F activity ratio. For the Fregeneda-Almendra Li-mica-rich pegmatites, this could be explained by a decrease of melt H2O solubility due to a relatively low pressure of emplacement.