The performance of waterborne polymer-polymer composite materials strongly depends on the particle morphology, but the precise quantitative characterization of complex morphologies is a long-standing problem. In this work, high angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) has been used to obtain a 3D quantitative characterization of the morphology of polymer polymer particles. The potential of this technique was demonstrated in the study of the effect of process variables (T-g of the seed, type of initiator, and instantaneous conversion of the monomer) on particle morphology during the semicontinuous emulsion copolymerization of styrene and butyl acrylate on methyl methacrylate-rich seeds. This analysis unveiled new mechanisms of morphology development.