Polymer-polymer composite nanoparticles allow both the improvement of the performance in established applications of waterborne polymer dispersions and targeting new applications that are out of reach of currently available products. The performance of these materials is determined by the particle morphology. To open the way to process optimization and on-line control of the particle morphology, the capability of the recently developed model to predict the evolution of the particle morphology during seeded semibatch emulsion polymerization process was evaluated. Structured polymer particles were synthesized by copolymerization of styrene and butyl acrylate (St-BA) on methyl methacrylate and butyl acrylate (MMA-BA) copolymer seeds of different glass transition temperature (Tgs). The model captured well the effect of process variables on the evolution of the particle morphology, opening the way to the design and implementation of optimal strategies.