A fundamental understanding of the behavior of gold (Au) nanostructures deposited on functional surfaces is imperative to discover and leverage interface-related phenomena that can boost the efficiency of existing electronic devices in sensorics, catalysis, and spintronics. In the present work, Au layers with nominal thickness of 2 nm were sputter-deposited on graphenized SiC substrates represented by buffer layer (BuL)/4H-SiC and monolayer epitaxial graphene (MLG)/4H-SiC. Morphometric analysis by means of scanning electron microscopy shows that Au on BuL self-assembles in nearly round-shaped plasmonically active islands, while on MLG, a fractal growth of considerably larger and ramified islands is observed. To correlate the experimentally established differences in surface morphology on the two types of graphenized substrates with energetics and kinetics of Au nanostructure growth, the deposit–substrate interaction strength was studied using density functional theory (DFT) calculations, molecular dynamics simulations, and optical measurements. The theoretical considerations involve participation of Au clusters with different sizes and energetics at the initial stages of the metal nanostructure formation. The results indicate that gold exhibits a considerably stronger interaction with BuL than with MLG, which can be considered as a key aspect for explaining the experimentally observed morphological differences. From the statistical analysis of Raman spectra, indications of Au intercalation of MLG are discussed. The current research shows that, due to its unique surface chemistry, buffer layer has peculiar affinity to gold when compared to other atomically flat surfaces, which is beneficial for boosting high-performance catalytic and sensing technologies based on low-dimensional materials.