The Spanish Central System (SCS) batholith, located in the Central Iberian Zone, is one of the largest masses of granite in the European Variscan Belt. This batholith is a composite unit of late- and post-kinematic granitoids dominated by S- and I-type series granite, with subordinate leucogranite and granodiorite. Zircon trace element contents, from two representative S-type and three I-type granitoids from the eastern portion of the SCS batholith, indicate a heterogeneous composition due to magma differentiation and co-crystallisation of other trace element-rich accessory phases. In situ, U-Pb dating of these zircons by SHRIMP and LA-ICP-MS shows 479-462-Ma inherited zircon ages in the I-type intrusions, indicating the involvement of an Ordovician metaigneous protolith, while the S-type intrusions exclusively contain Cadomian and older zircon ages. The zircon crystallisation ages show that these granites have been emplaced at ca. 300 Ma with a time span between 303 ± 3 Ma and 298 ± 3 Ma. Precise dating by CA-ID-TIMS reveals a pulse at 305. 7 ± 0. 4 Ma and confirms the major pulse at 300. 7 ± 0. 6 Ma. These ages match the Permo-Carboniferous age for granulite-facies metamorphism of the lower crust under the SCS batholith and coincide with a widespread granitic event throughout the Southern Variscides. Ti-in zircon thermometry indicates temperatures between 844 and 784°C for both the S- and I-type granites, reinforcing the hypothesis that these granites are derived from deep crustal sources.