We employ a combination of the single chain in mean field simulation approach with the solution of Poisson's equation to study the influence of charge heterogeneities on the structure of protein–polyelectrolyte complexes. By adopting a coarse-grained model of representing proteins as charged nanoparticles, we studied the influence of the pattern of charge heterogeneities, net charge, ratio of positive to negative charges on the patches, and the volume fraction of the particles on the structural and aggregation characteristics of proteins in polyelectrolyte solutions. Our results demonstrate that the pattern of charge heterogeneities can exert a significant influence on the resulting characteristics of the aggregates, in some cases leading to a transformation from polymer-bridged complexes into direct particle aggregates driven by the attraction between oppositely charged patches.