Partial acetylation of the amine-terminated poly(amidoamine) dendrimer has been used in the preparation of dendrimer particles conjugated with a wide variety of functional ligands including targeting moieties, therapeutic agents, and dye molecules. The effectiveness of mass transport during the partial acetylation reaction was found to have a major effect on subsequent distributions of dendrimer ligand components and to be a major source of inconsistency between batches. This study has broad implications for a wide range of nanoparticle-ligand systems because it demonstrates that conjugates with the same mean ligand-particle ratios can have completely different distribution profiles.