The innermost domain of the autochthon of the Iberian Massif (Central Iberian Zone) consists of Upper Proterozoic–Lower Cambrian metasedimentary rocks and Early Paleozoic augen gneisses. The former were intruded by mafic magmas as small bodies that later became amphibolites under Variscan metamorphism, gabbro-diabasic textures being sometimes well preserved. Three main groups of amphibolites can be established: (A) the light rare earth element (LREE)-depleted group, characterized by an extremely low rare earth element (REE) fractionation factor [(La/Lu)_CN = 0.27–0.34] and low Ti content; (B) the flat REE pattern group, characterized by a small REE fractionation factor [(La/Lu)_CN small REE fractionation factor [(La/Lu)_CN = 0.95–1.25]; and (C) the LREE-enriched group, characterized by a strong fractionation factor [(La/Lu)_CN = 3.53–15.04] and high Ti content. Regular major element variations for the depleted amphibolites point to a low-pressure fractional crystallization as the major process, the strongly depleted amphibolites considered to be parent magmas, although crustal contamination accounts for their broad Nd and Sr isotope ranges as well as trace element variations. Part of the enriched amphibolite samples have an ocean island basalt–like signature and plot within the mantle array, suggesting a mantle mixed source. Other samples show decoupling of Nd and Sr isotopic systems as a response to a probable mixing process involving fluid-rock interaction during subsolidus evolution, which is supported by their high δ¹⁸O values. Geochemical characterization of amphibolite groups is consistent with an extensional within-plate tectonic setting, whereas processes involved may account for a similar mantle-crust interaction that occurred throughout the entire Central Iberian Zone and probably all over the northern margin of Gondwana during late Neoproterozoic–Early Paleozoic times.