Synthesis of spherical, biocompatible nanoparticle aggregates using a small molecular cross-linker is a simple and flexible approach for the controlled assembly of gold nanoparticles. This strategy can be extended to a variety of cross-linkers, making it possible to the test the effect of cross-linker properties on aggregate formation and physicochemical properties. Here, we synthesized aggregates using a series of structurally homologous cross-linkers with differing valencies. These aggregates have the same size, morphology, surface charge, surface coating, and stability in salt, media, and low pH conditions, but they differ in their stability to cyanide etching and uptake by cells. This highlights the fine-tuning of nanoparticle aggregate properties that can be achieved by using small-molecule cross-linkers.