Olivine-rich troctolites (>70% olivine) reveal that extensive melt impregnation of pre-existing olivine-rich lithologies participate to the building of slow spread oceanic crust. To constrain their origin and their impact on the structure and geochemistry of oceanic crust, we realized a multi-scale petro-structural, geochemical, and numerical modeling study of olivine-rich troctolites drilled at IODP Hole U1309D (Atlantis Massif, Mid-Atlantic Ridge 30°N). Discrete intervals of olivine-rich troctolites display sharp to diffuse contacts with neighboring troctolites or gabbros. Their texture is characterized by plastically deformed (high temperature imprint), corroded coarse-grained to undeformed fine-grained olivine embayed in poikilitic clinopyroxene and plagioclase. Olivine crystallographic preferred orientations show weak [001] clusters. Olivine has variable major and minor element compositions, but similar fractionated REE (DyN/YbN = 0.04–0.11). We distinguished three types of olivine-rich troctolites based on microstructure, texture and mineral composition. Olivine-rich troctolites 1 and 2 display sharp contacts with adjacent lithologies. Type 1 has modal olivine <75%, occurring mainly as single rounded grains with primitive compositions (Mg# = 85–86), and associated with high Mg# clinopyroxene. Type 2 has higher olivine modes (>75%), dominantly forming aggregates, showing more evolved compositions (Mg# = 83–84) and associated with slightly lower Mg# clinopyroxene. These variations of olivine modes and compositions are in contrast to common trends of magmatic crystallization that predicts decreasing modal olivine with melt differentiation towards evolved compositions. Type 3 has diffuse contacts with gabbroic veins and modal olivine overlapping those of types 1 and 2. Chemical traverses along principal crystallographic axes of olivine are flat, suggesting local equilibrium between olivine and neighboring phases. Mineral modes and compositions, together with textures and microstructures, suggest that olivine-rich troctolites formed after melt-rock interactions in a reactive porous flow process. Their compositions are best modeled by percolation of primitive MORBs into Hole U1309D impregnated and compositionally heterogeneous harzburgites, triggering orthopyroxene dissolution, followed by olivine assimilation and concomitant crystallization of clinopyroxene and plagioclase. Modeling shows that Ni variations in olivine at constant Mg# are mantle inherited. Compositions of olivine-rich troctolite 1 are fitted assuming higher olivine assimilation (Ma = 0.06–0.13) in contrast to olivine-rich troctolites 2 and 3 (Ma = 0.01–0.02). Olivine-rich troctolite 3 was ‘buffered’ by crystallizing reacted melts, progressively more evolved as temperature decreased during a late stage process. We interpret olivine-rich troctolites from the Atlantis Massif as marking local assimilation of harzburgitic mantle into the gabbroic sequence during a period of enhanced magmatism at depth. Our study shows that the distribution and variable compositions of olivine-rich troctolites result from the incipient stages of this process when local spatial variations in mantle rock permeability, probably related to pyroxene distribution, controlled in turn melt transport and mantle-melt interactions.