Abstract Well-preserved primary contact relationships between a Late Proterozoic metasedimentary and the metagranitic core and Palaeozoic cover series of the Menderes Massif have been recognized in the eastern part of the Çine submassif on a regional-scale. Metaconglomerates occur as laterally discontinuous channel-fill bodies close the base of the metaquartzarenite directly above the basement. The pebbles in the metaconglomerates consist mainly of different types of tourmaline-rich leucocratic granitoids, tourmalinite and schist in a sandy matrix. Petrographic features, geochemical compositions and zircon radiometric ages (549.6 ± 3.7–552.3 ± 3.1 Ma) of the diagnostic clasts of the metaconglomerates (e.g. leucocratic granitoids and tourmalinites) show excellent agreement with their in situ equivalents (549.0 ± 5.4 Ma) occurring in the Pan-African basement as stocks and veins. The correlation between clasts in the metaconglomerates and granitoids of the basement suggests that the primary contact between the basement and cover series is a regional unconformity ( supra-Pan-African Unconformity) representing deep erosion of the Pan-African basement followed by the deposition of the cover series. Hence the usage of ‘core–cover’ terminology in the Menderes Massif is valid. Consequently, these new data preclude the views that the granitic precursors of the leucocratic orthogneisses are Tertiary intrusions.