The synthesis of semiconductor nanocrystals with controlled doping is highly challenging, as often a significant part of the doping ions are found segregated at nanocrystals surface, even forming secondary phases, rather than incorporated in the core. We have investigated the dopant distribution dynamics under slight changes in the preparation procedure of nanocrystalline ZnO doped with manganese in low concentration by electron paramagnetic resonance spectroscopy, paying attention to the formation of transient secondary phases and their transformation into doped ZnO. The acidification of the starting solution in the co-precipitation synthesis from nitrate precursors lead to the decrease of the Mn2+ ions concentration in the core of the ZnO nanocrystals and their accumulation in minority phases, until ~79% of the Mn2+ ions were localized in a thin disordered shell of zinc hydroxynitrate (ZHN). A lower synthesis temperature resulted in polycrystalline Mn-doped ZHN. Under isochronal annealing up to 250 °C the bulk ZHN and the minority phases from the ZnO samples decomposed into ZnO. The Mn2+ ions distribution in the annealed nanocrystals was significantly altered, varying from a uniform volume distribution to a preferential localization in the outer layers of the nanocrystals. Our results provide a synthesis strategy for tailoring the dopant distribution in ZnO nanocrystals for applications ranging from surface based to ones involving core properties.