The ultramafic–mafic complexes located at the base of obducted paleo-island arcs are commonly interpreted as evidence for intra-crustal fractionation of primitive (high-Mg#) mantle melts. The present study, realized on the Jijal mafic–ultramafic basal section of the Cretaceous Kohistan oceanic arc (N Pakistan), discards a crystal fractionation model from a single parental magma to take into account the geochemical and isotope variations observed between the plutonic crust and the underlying ultramafic section. The basal ultramafic rocks, i.e. dunites, wehrlites and clinopyroxenites, show high Mg#, extremely depleted REE patterns, no marked HFSE anomalies and high LILE enrichment. Cpx and leached whole rocks from this unit yield restricted εNd values (+ 5.5 to + 6.8), a large εSr range (− 5.9 to + 8.8) and mainly radiogenic 207Pb/204Pb ratios. The overlying mafic section, i.e. gabbroic rocks, displays low Mg# (46 < Mg# < 54), enriched REE patterns and marked HFSE anomalies. These plutonic rocks have also very homogeneous Sr and Pb isotopic compositions defining a restricted domain, which does not overlap that of the ultramafic samples. Moreover, Cpx from the basal ultramafics yield an Sm–Nd isochron at 117 ± 7 Ma interpreted as dating crystallization of the ultramafic section. Together, these results indicate that the mafic rocks on one hand and the ultramafic rocks on the other hand, originate from separate sources with specific emplacement underneath the subduction zone. A lherzolite lens, collected from the top of the mafic section, plots on the early Cretaceous Sm–Nd isochron and therefore yields the same 143Nd/144Nd initial ratio. This suggests that the ultramafic part of the lower Kohistan arc complex sampled the initiation stages of the subduction with production of magmas with boninite-like features. At this stage, the mantle wedge has been already modified by percolation of the first slab-derived fluids. On such a scenario the lherzolite lens would correspond to the lithospheric mantle underneath the arc before its initiation. A multi-stage history is proposed for the evolution for the Kohistan arc through not, vert, similar 30 Ma. Stage #1 reflects the spontaneous initiation of subduction associated with extensive boninitic affinity magmatism, stages #2 and #3 are related to arc building by tholeiitic melts and, a fourth step (stage #4) corresponds to the intra-crustal differentiation.