Peptide and protein labelling methods have been under continuous development over the last few decades. Labelled proteins and peptides are undoubtedly indispensable for the study of biological processes at a molecular level. Nowadays, labels can be obtained via a plethora of different routes using native as well as non-native functionalities present or deliberately incorporated into the biomolecule of interest. Often, peptide ligand–protein interactions or multimeric protein complexes are involved in biological cascades of many different types and the development of efficient and site-selective crosslinking methods for freezing those transient interactions has been essential in furthering our understanding of the intricate details of cell-based machineries. Given the event of next generation, biologicals-based drug design, this research and its applications have now even reached the pharmaceutical development stage with antibody–drug conjugates (often referred to as ADCs) at the forefront of modern targeted delivery approaches. In the current chapter, we aim to provide a comprehensive overview of the most important strategies towards the generation of proteins and peptides modified in a genuine site-selective (as opposed to amino-acid selective) way as well as the application of some of those and alternative methodologies in the generation of site-specifically and covalently crosslinked peptide ligand–protein and protein–protein complexes.