This study investigates encapsulation efficiency of model drug, encapsulated by magnetic poly D, L-lactic-co-glycolic acid (PLGA) nanoparticles (NPs). This is the following part of our preceding paper, which is referred in this paper as Part I. Magnetic nanoparticles and model drug human serum albumin (HSA)-loaded PLGA NPs were prepared by the double emulsion solvent evaporation method. Among five important process variables, concentration of PLGA and concentration of HSA in the inner aqueous phase along with their cross-effect had the strongest influence on the encapsulation efficiency. Encapsulation efficiency of nanoparticles ranged from 18% to 97% depending on the process conditions. Higher encapsulation efficiencies can be achieved by using low HSA and high PLGA concentrations. The optimization process, carried out by exact mathematical tools using GAMSTM/MINOS software makes it easier to find out optimum process conditions to achieve comparatively high encapsulation efficiency (e.g. 92.3%) for relatively small-sized PLGA NPs (e.g. 155 nm).