The immobilization of metal nanoparticles (NPs) with molecular control over their organization is challenging. Herein, we report the formation of molecularly cross-linked AuNP assemblies using a layer-by-layer approach. We observed four types of assemblies: 1)?small aggregates of individual AuNPs, 2)?large aggregates of individual AuNPs, 3)?networks of fused AuNPs, and 4) gold islands. Interestingly, these assemblies with the different cross-linkers and capping layers represent different stages in the complete fusion of AuNPs to afford islands of continuous gold. We demonstrate that the stability toward fusion of the nanoparticles of the on-surface structures can be controlled by the reactivity of the cross-linkers and the hydrophilicity/hydrophobicity of the nanoparticles.