The present study provides data on the high-grade metamorphic basement of the Serbo-Macedonian Massif (SMM) that is exposed in Ograzhden and Belasitsa Mountains, SW Bulgaria. We combined the conventional ID-TIMS with the in-situ LA-ICP-MS U-Pb zircon dating and compiled them with petrological and geochemical studies to better constrain the age and origin of the protoliths and the grade of metamorphic overprint. The orthogneisses are dated in the range of 450–455 Ma, except for the Kolarovo metagranites, which define two clusters of age data at 554.8 ± 3.3 Ma and 510.2 ± 3.5 Ma. We assume sedimentary origin for the plagiogneisses that show zircon population and age distribution similar to the gneiss-schists: main peak at ~600 Ma and minor populations at 700–800 Ma, 1000–1100 Ma and 2400 Ma. The amphibolites yield the youngest precursor ages of 435–440 Ma. The whole succession of rocks is metamorphosed to upper amphibolite facies conditions, with peak temperatures (Tmax) between 675–710 °C in Ograzhden Mountain and at ~650 °C in Belasitsa Mountain. Pressure estimates (Pmin) range from 6–8 kbar to 12–13 kbar, based on 3T phengite relics and application of different calibrations of phengite barometer. However, higher pressures cannot be excluded due to evidence from the eclogitic metabasites. The metamorphism has been dated in zircon rims of metasediments, vein rocks and amphibolites, as well as in xenotime of newly formed leucosome, at ~330 Ma. The wide range of primary rocks, their major- and trace-element chemistry and Sr-Nd isotope signature, combined with the age data of zircon populations, give evidence for an old crustal fragment with Gondwana affinity that was rejuvenated in the Ordovician–Silurian, before the collision and metamorphic overprint during the Variscan orogeny.