Bimolecular fluorescence complementation is a method of probing protein-ligand interactions under physiological conditions. It provides a state-of-the-art tool to examine interactions observed in 3D structures of multi-component protein complexes, either to validate new experimental structures or to assess the correctness of homology models. Applications of the method range from homo- and hetero-oligomeric assemblies, including non-protein-ligands. Proof-of-principle experiments have also shown the potential of bimolecular fluorescence complementation to monitor protein complexes in a conformation-dependent manner. Here, recent highlights of structure-based applications of the method are outlined and assessed in terms of project-specific findings. These examples demonstrate the power of bimolecular fluorescence complementation to become a leading analysis tool in structural biology, to independently evaluate and characterize higher-order protein complexes.