In this work, water-dispersible Mn:ZnSe/ZnO core/shell quantum dots (QDs) with pure dopant emission were prepared via a two-step method. Compared with the traditional organometallic approach, this two-step method has many advantages, such as using low-cost and non-toxic chemicals, low reaction temperature and simple operation. Moreover, the obtained Mn:ZnSe/ZnO core/shell QDs also showed superior properties to those prepared by the aqueous solution synthesis, such as narrow emission and good monodispersity. The influence of the storage time of Mn:ZnSe QDs in organic medium, the amount of MPA and temperature during the period of ZnO shell deposition on the photo-luminescence (PL) properties was investigated. Under optimal conditions, MPA-capped Mn:ZnSe/ZnO QDs with an average diameter of 2.6 nm and a dopant PL quantum yield (QY) of 30% in water were produced.