Sediments incorporated into accretionary prisms experience significant changes in physical properties, grain fabric, and diagenesis. The record of such changes is preserved in sediment microstructures. Scanning electron microscopy (SEM) analyses were carried out on sediments collected from within and seaward of the Nankai accretionary prism to document microstructural changes with depth, lithology, and discrete deformation during the earliest stages of tectonic deformation. Clay mineral preferred orientations (CPOs) increased with depth due to burial, inclined CPOs were evident adjacent to discrete deformation structures and within the accretionary prism, reflecting the influence of sub-horizontal tectonic stress with accretion. Mineralogical and microstructural contrasts across the decollement and the seaward proto-decollement suggest strength differences that may help to localize the fault at this location.