We report the engineering of surface ions present as defects in doped quantum dots (Qdots) following their synthesis. This was achieved by treating the Qdots with cation-exchange resin beads (CB). An aqueous dispersion of Mn2+-doped ZnS Qdots, when treated with different amounts of CB, resulted in two kinds of changes in the emission due to Mn2+ ions. First, the intensity increased in the presence of a smaller amount of CB, to the extent of a doubled quantum yield. With increased CB as well as incubation time, the emission intensity decreased systematically, accompanied by an increasing blue shift of the peak emission wavelength. Electron spin resonance results indicated the removal of clusters of Mn2+ present in the Qdots by the CB, which has been attributed to changes in the emission characteristics. Transmission electron microscopy studies revealed that for smaller amounts of CB there was no change in the particle size, whereas for greater amounts the particle size decreased. The results have been explained on the basis of the removal of Mn2+ (and also Zn2+) ions present on the surfaces of Qdots in the form of clusters as well as individual ions.