We utilize atomistic molecular dynamics (MD) simulations to study local structural changes inside a polyelectrolyte complex consisting of poly(styrenesulfonate) (PSS) and poly(diallyldimethylammonium) (PDADMA) upon densification, in analogy to ultracentrifugation in experiments. In particular, we focus on the water content and on the reinforcement of the PSS–PDADMA network for various external accelerations. We demonstrate that apart from the formation of mesoscopic pores observed experimentally also the microscopic structure and the local relaxation processes likely affect the unique rheological properties of compacted polyelectrolyte complexes, as densification increases both the number of PSS–PDADMA coordinations and the intermixing of PSS and PDADMA. These processes slow down local rearrangements, thus further stabilizing the compacted state. We find that the concept of binary PSS–PDADMA salt bonds—relevant for theoretical models—is not strictly valid in the dense limit.