The synthesis of metal nanoparticle (NP) assemblies stabilized by functional molecules is an important research topic in nanoscience, and the ability to control interparticle distances and positions in NP assemblies is one of the major challenges in designing and understanding functional nanostructures. Here, two series of functionalized adamantanes, bis-adamantanes, and diamantanes, bearing carboxylic acid or amine functional groups, were used as building blocks to produce, via a straightforward method, networks of ruthenium NPs. Both the nature of the ligand and the Ru/ligand ratio affect the interparticle distance in the assemblies. The use of 1,3-adamantanedicarboxylic acid allows the synthesis of three-dimensional (3D) networks of 1.7–1.9 nm Ru NPs presenting an interparticle distance of 2.5–2.7 nm. The surface interaction between Ru NPs and the ligands was investigated spectroscopically using a 13C-labeled ligand, as well as theoretically with density functional theory (DFT) calculations. We found that Ru species formed during the NP assembly are able to partially decarbonylate carboxylic acid ligands at room temperature. Decarbonylation of a carboxylic acid at room temperature in the presence of dihydrogen usually occurs on catalysts at much higher temperatures and pressures. This result reveals a very high reactivity of ruthenium species formed during the network assembly. The Ru NP networks were found to be active catalysts for the selective hydrogenation of phenylacetylene, reaching good selectivity toward styrene. Overall, we demonstrated that catalyst activity, selectivity, and NP network stability are significantly affected by Ru NP interparticle distance and electronic ligand effects. As such, these materials constitute a unique set that should allow a better understanding of the complex surface chemistry in carbon-supported metal catalysts.