Protein–protein interactions are central to many biological processes. A considerable challenge consists however in understanding and deciphering when and how proteins interact, and this can be particularly difficult when interactions are weak and transient. The site‐specific incorporation of unnatural amino acids (UAAs) that crosslink with nearby molecules in response to light provides a powerful tool for mapping transient protein–protein interactions and for defining the structure and topology of protein complexes both in vitro and in vivo. Complementary strategies consist in site‐specific incorporation of UAAs bearing electrophilic moieties that react with natural nucleophilic amino acids in a proximity‐dependent manner, thereby chemically stabilizing low‐affinity interactions and providing additional constraints on distances and geometries in protein complexes. Herein, we review how UAAs bearing fine‐tuned chemical moieties that react with proteins in their vicinity can be utilized to map, study, and characterize weak and transient protein–protein interactions in living systems. Trapping transient protein–protein interactions: Site‐specific incorporation of unnatural amino acids bearing chemical groups that allow covalent crosslinking with molecules in their vicinity provides a powerful tool for mapping weak and transient protein–protein interactions and for defining the structure and topology of protein complexes both in vitro and in vivo.