Notable within-crystal variability of mineralogical and geochemical properties of single natural diamonds are commonly attributed to changing chemistry of parental fluids, sources of carbon and redox conditions of diamond precipitation. A distinct type of compositional heterogeneity (mixed-habit structure) is well-known to occur in diamonds as well as in many other minerals due to purely “structural” reasons that are unequal crystal chemistry of crystallographically different faces and selective absorption and fractionation of impurities between adjacent growth pyramids. Based on the combined cathodoluminescence, Fourier-transformed infrared spectroscopy and photoluminescence spectroscopy, study of nine diamond crystals with different growth histories and external morphology, but all showing mixed-habit patterns at different growth stages, we show that mixed-diamonds may grow in closed system conditions or with a slowly decreasing growth rate from a media with a much lower impurity content than previously thought. Intracrystal nitrogen distribution seems to be a function of growth rate even in the cases of unusual impurity partitioning between growth sectors. Generally poor with IR-active hydrogen at moderate nitrogen aggregation parameters, studied diamonds likely resemble the low hydrogen content from the growth medium that, for cubic diamonds, was typically suggested hydrogen-rich and a crucial factor for growth of cubic and mixed-habit diamonds. We also show that mixed-habit diamond growth may occur not only in peridotitic suite but also in an extended field of geochemical affinities from high-Ni to low-Ni or maybe even Ni-free environments, such as pyroxenitic or eclogitic.