The oceanic crust crystallizes from melts formed within a heterogeneous mantle source, which is mostly composed of variably depleted peridotites and recycled crust. Yet, the compositional variability of this mantle source and the progressive aggregation of heterogeneous melts during extraction are poorly constrained. Here, we show that in situ isotopic analyses in gabbros formed at the East Pacific Rise retain substantially greater Sr-Nd-Hf isotopic heterogeneity than basalts erupted along the fast-spreading ridge. This implies that melt aggregation during migration through the upper mantle and lower crust is inefficient, even at magmatically productive spreading ridges; efficient melt mixing likely occurs in the overlying axial melt lens. Local isotopic heterogeneity of Hess Deep gabbros indicates incomplete mixing of primary melts produced from variably depleted peridotites and oceanic crust recycled at least 1.5 billion years ago. The isotopic heterogeneity recorded in lower gabbros further substantiates that basalt compositions reflect only part of the compositional spectrum of melts passing through the ridge plumbing system.