AbstractMagma migration and differentiation processes are key to understanding the development and evolution of oceanic magma reservoirs. To provide new quantitative geochemical constraints on these processes, we applied a high‐resolution approach to study an interlayered section of the lower oceanic crust sampled at Atlantis Bank, on the (ultra)slow‐spreading Southwest Indian Ridge. The section is characterized by sharp grain‐size layering between fine‐ and coarse‐grained olivine gabbros that is representative of other layered structures described at the Atlantis Bank oceanic core complex. The textures and fabrics of the layers and the nature of their contacts indicate formation by intrusion of a magma (i.e., crystal‐bearing) into an almost solidified coarse‐grained mush. Petrographic observations and in situ incompatible trace element signatures indicate that the fine‐ and coarse‐grained layers record reactive porous migration of melts. Widespread reactive porous flow occurred prior to intrusion within the coarse‐grained gabbro, producing mineral compositions enriched in incompatible elements. The intrusive fine‐grained lithology records a late stage event of localized reactive melt percolation in cm‐scale structures, which lead to strong light rare earth elements depletion relative to heavy rare earth elements. In addition, we highlight the occurrence of interactions at the contacts between layers and partial modification in compositions of the intruded lithology. This layered section likely represents a contact between two larger magma bodies emplaced within the lower crust during accretion, where the type of melt migration (intrusion or porous flow) and the modalities of melt percolation (widespread or localized) strongly govern the composition of the crustal lithologies.