The inert gas condensation method (IGC) produces multimetallic nanoparticles in a metastable state that may exhibit heterogeneities of size, structure, and composition. The deposition of IGC-fabricated nanoparticles on substrates allows for a detailed characterization by combination of aberration-corrected scanning transmission electron microscopy (TEM) and atom probe tomography (APT). Multiple particle monitoring and high-resolution scanning TEM give access to the size distribution of Au-Cu nanoparticles (<10 nm in diameter, bimodal distribution). TEM and APT show that the alloying between Cu and Au may stabilize the Ih structure for smaller particles (<4 nm). Combining high-resolution scanning transmission electron microscopy/energy dispersive X-ray and three-dimensional composition analysis by APT reveals that an excess of Cu may be present in a shell around the larger particles (>7 nm), while Cu is more randomly distributed in smaller particles.