We provide results of a comprehensive mineralogical and microstructural study of relict lherzolites of the main ore field and fresh rocks from a deep structural borehole drilled in the south-eastern part of the Kempirsay massif. Olivine and orthopyroxene from lherzolites contain numerous pieces of evidence of material redistribution at different scales caused mainly by solid-state processes, such as plastic flow of mantle, syntectonic recrystallization, and annealing. The results of deformation-induced processes at the submicron scale are recorded by optical and electronic microscopy. In olivine, the plastic deformation caused segregation of impurities at structural defects. As a result, abundant tiny rods of newly formed Cr-spinels occurred inside its grains. Moreover, in enstatite, deformation caused partial or complete chemical decomposition with exsolution of diopside, pargasite and spinel lamellae up to the formation of a “fibrous” structure. In other cases, it provided partial or complete recrystallization to form new phases of enstatite-2, forsterite, diopside, pargasite, and spinel. Petrographic observations are validated by geochemical data, i.e., regularly decreasing concentrations of minor elements in neoblasts compared to large grains (porphyroclasts). Further redistribution of spinel grains with the formation of chromitite bodies is witnessed by their permanent association with the most mobile phase of the upper mantle, i.e., olivine, which is the only mineral that remains stable under the intense plastic flow. An increased concentration of Cr-spinel grains during formation of massive chromitites could appear under conditions close to pressure sintering, as evidenced by stressed textures of ores and an increased grain size compared to disseminated chromitites. The formation of unique chromitite deposits is associated with integration of numerous disparate podiform bodies into “ore bunches” due to the tectonic impact in the shear-compression regime. This was most likely associated with transition of the rifting (spreading) regime to that of the upper mantle of the fore-arc basin.