We report the identification, description, and role of multinuclear metal-thiolate complexes in aqueous Au-Cu nanoparticle syntheses. The structure of these species was characterized by nuclear magnetic resonance spectroscopy, mass spectrometry, X-ray photoelectron spectroscopy, and X-ray absorption spectroscopy techniques. The observed structures were found to be in good agreement with thermodynamic growth trends predicted by first-principles calculations. The presence of metal-thiolate complexes is then shown to be critical for the formation of alloyed Au-Cu architectures in the small nanoparticle regime (diameter ∼2 nm). In the absence of mixed metal-thiolate precursors, nanoparticles form with a Cu-S shell and a Au-rich interior. Taken together, these results demonstrate that prenucleation species, which are discrete molecular precursors distinct from both initial reagents and final particle products, may provide an important new synthetic route to control final metal nanoparticle composition and composition architectures.