The Neoarchean to Paleoproterozoic Betsiboka Suite of Madagascar mainly consists of granitoid orthogneiss and migmatite variably metamorphosed to amphibolite and granulite facies during the late Neoproterozoic. New U–Pb zircon data yield emplacement ages of 2512 ± 17, 2507 ± 17, 2493 ± 14 and 2485 ± 16 Ma. Zircon δ¹⁸O data indicate involvement of the continental crust during magma genesis. Mostly positive ε_Hf(t) values plot slightly below the depleted-mantle curve. The isotopic data favour mixing between an older Archean crustal source and a juvenile depleted-mantle source. Possible local crustal candidates for the older component in the exposed Malagasy basement are Neoarchean mafic gneisses in the Tsaratanana Complex and the c. 3200 Ma Nosy Boraha orthogneiss in the Antongil Domain. The new isotopic data support interpretations from previous studies investigating the genesis of Tonian plutonic rocks advocating crustal melting of a Mesoarchean crustal source in the Antananarivo Domain. In addition, detrital zircon in the Proterozoic Ambatolampy Group and Itremo Group probably had a local source with the same isotopic composition as the Betsiboka Suite. Our study demonstrates the significance of multi-isotopic data from zircon for constraining the sources of detrital zircon grains in sedimentary provenance studies.