We examine mid-lower crustal xenoliths erupted in Late Pleistocene to Holocene alkali basalt at San Quintin, Baja California, Mexico to investigate the role of partial melt in deep lithospheric deformation. Using major and trace element mineral chemistry data obtained from LA-ICP-MS and microstructural data obtained from EBSD, we cluster the crustal xenoliths into two groups based on textural and geochemical characteristics: Group (1) largely unfoliated two-pyroxene gabbros with minor amounts of olivine, and Group (2) gabbros with strong compositional foliation and up to 30% modal olivine. We interpret Group 1 xenoliths as representing underplated cumulates from basaltic magmas, whereas petrographic and quantitative microstructural data suggest Group 2 xenoliths record melt infiltration of pre-existing gabbros coeval with deformation, perhaps in a deep crustal shear zone. We propose this shear zone represents a deep lithospheric expression of the active transform plate boundary along the Baja California margin.