The stability of nanoparticle suspensions and the details of their agglomeration depend on the interactions between particles. We study this relationship in gold nanoparticles stabilized with different alkyl thiols in heptane. Temperature-dependent interactions were inferred from small-angle x-ray scattering, agglomeration kinetics from dynamic light scattering, and agglomerate morphologies from transmission electron microscopy. We find that the particles precipitate at temperatures below the melting temperatures of the dry ligands. Agglomerates grow with rates that depend on the temperature: Around precipitation temperature, globular agglomerates form slowly, while at lower temperatures, fibrilar agglomerates form rapidly. All agglomerates contain random dense packings rather than crystalline superlattices. We conclude that ligand-ligand and ligand-solvent interactions of the individual particles dominate suspension stability and agglomeration kinetics. The microscopic packing is dominated by interactions between the ligands of different nanoparticles.