Correlation of catalyst structure with activity is foundational to the rational design of transition metal catalysts. While X-ray crystallography routinely provides structural characterization of kinetically stable pre-catalysts and intermediates, experimental elucidation of the structures of reactive intermediates, which are the species intimately engaged in bond-breaking and -making in catalysis, is generally not possible due to the transient nature of these species. Here, we demonstrate in crystallo synthesis of Rh2 nitrenes that participate in catalytic C–H amination, and characterization of these transient intermediates as triplet adducts of Rh2. Further, we observe the impact of coordinating substrate, which is present in excess during catalysis, on the structure of transient Rh2 nitrenes involved in C–H amination. By providing structural characterization of authentic C–H functionalization intermediates, and not kinetically stabilized model complexes, these experiments provide the opportunity to define critical structure-activity relationships.