We analyzed high-quality seismic reflection profiles across the ocean-continent transition in the Enderby Basin between the Kerguelen Plateau and the Antarctic margin. There, we observe numerous high-amplitude dipping reflections in the lower oceanic crust which was accreted at a magmatic spreading center as testified by the almost uniform 6.4-7 km thick crust and its unfaulted, flat top basement. The deep reflections are rooting onto the Moho and are dipping both ridgeward and continentward. They occur in dense networks in mature oceanic crust as well as close to the continentward termination of oceanic crust and in the ocean-continent transition zone. The comparison with field observations in the Oman ophiolite suggests that these lower crustal dipping reflectors could correspond to syn-magmatic faults. In Oman, very high temperature (up to syn-magmatic), high temperature (sub-solidus plastic deformation) and low temperature (brittle) deformation coexist along the same fault over distances of a few hundred meters at Moho level. This very high temperature gradient may be explained by the sudden and intense interaction between crystallizing magmas and hydrothermal fluids induced by the episodic nucleation of faults in a context of continuous magmatic spreading. The igneous layering becomes extremely irregular compared to its monotonous sub-horizontal orientation away from the faults which, together with enhanced hydrothermal alteration restricted to the fault zones, might change the physical properties (velocity, density) and increase the reflectivity of syn-magmatic faults. We further speculate that these processes could explain the brightness of the lower crustal dipping reflectors observed in our seismic reflection data. Both the seismic reflection profiles of the Enderby Basin and the Oman ophiolite show evidence for syn-accretion tectonism at depth together with the systematic rotation of originally horizontal lava flows or originally vertical dikes, pre-dating cessation of magmatic activity. This indicates ubiquitous deformation processes within the axial zone of magmatic spreading centers.