In this work, we have employed a suite of complementary analytical techniques to shed light on the nanocomposite structures formed during gold nanoparticles (AuNPs) synthesis in the presence of poly(amidoamine) (PAMAM) dendrimers. Nanocomposites of AuNPs and either fourth or eighth generation amine-terminated PAMAM dendrimers (G4 or G8) were prepared. The size distributions of AuNPs and the nanocomposites were determined by transmission electron microscopy. Atomic force microscopy phase imaging and neutral impact collision ion scattering spectroscopy (NICISS) were utilized for the first time to investigate and compare nanocomposite structures formed from G4 and G8. Our results suggest that G4 stabilized the AuNP by capping the AuNP particle surface but that a certain fraction of the gold surface was still barely covered. In contrast, the metal nanoparticle surface was completely covered by G8. In addition, NICISS results provided evidence that nanocomposites deformed when being deposited directly onto a substrate.