The frontiers between homogeneous and heterogeneous catalysis are progressively disappearing. The decoration of transition metal nanoparticles (NPs) with ligands, also known as surface modifiers or capping agents, primarily allows NP size control but dramatically impacts activity and selectivity in catalysis. Computational tools have shown their capability of providing insight at atomic level in both homogeneous and heterogeneous areas but, due to the complexity of these interfaces, the underlying reaction mechanisms are often not described and certainly not well understood. In this mini-review, we describe the main challenges in modelling and survey the most recent computational studies that emphasise the role of ligands in tuning catalytic performance. We focus on density functional theory (DFT) simulations of the interfaces between transition metals (ruthenium, palladium, platinum, gold) and organic ligands (NHC, amine, phosphine, thiol), surfactants, and ionic liquids. Revealing the reaction pathways that operate at this hidden interface between homogeneous and heterogeneous worlds will provide guiding rules to design new systems that circumvent linear scaling relationships and foster a unified theory of catalysis.