Self-assembly of nanoscale structures at liquid-solid interfaces occurs in a broad range of industrial processes and is found in various phenomena in nature. Conventional theory assumes spherical particles and homogeneous surfaces, but that model is oversimplified, and nanoscale in-situ observations are needed for a more complete understanding. We used liquid phase scanning transmission electron microscopy (LP-STEM) to examine the interactions that direct the self-assembly of superlattices formed by gold nanoparticles (AuNPs) in non-polar liquids. Varying the molecular coating of the substrate modulated short-ranged attraction and led to switching between a range of different geometric structures including hexagonal close-packed (hcp), simple hexagonal (sh), dodecahedral quasi-crystal (dqc), and body-centered cubic (bcc) lattices, as well as random distributions. Langevin dynamics simulations explain the experimental results in terms of the interplay between nanoparticle faceting, ligand shell structure, and substrate-NP-interactions.