While atom tracking with isotope-labeled compounds is an essential and sophisticated wet-lab tool in order to, e.g., illuminate reaction mechanisms, there exists only a limited amount of formal methods to approach the problem. Specifically when large (bio-)chemical networks are considered where reactions are stereo-specific, rigorous techniques are inevitable. We present an approach using the right Cayley graph of a monoid in order to track atoms concurrently through sequences of reactions and predict their potential location in product molecules. This can not only be used to systematically build hypothesis or reject reaction mechanisms (we will use the mechanism “Addition of the Nucleophile, Ring Opening, and Ring Closure” as an example), but also to infer naturally occurring subsystems of (bio-)chemical systems. We will exemplify the latter by analysing the carbon traces within the TCA cycle and infer subsystems based on projections of the right Cayley graph onto a set of relevant atoms.