The use of fully or partially absorbing boundary conditions for diffusion-based problems has become paradigmatic in physical chemistry and biochemistry to describe reactions occurring in solutions or in living media. However, as chemical states may indeed disappear, particles cannot, unless such degradation happens physically and should thus be accounted for explicitly. Here, we introduce a simple, yet general idea that allows one to derive the appropriate boundary conditions self-consistently from the chemical reaction scheme and the geometry of the physical reaction boundaries. As an illustration, we consider two paradigmatic examples, where the known results are recovered by taking specific physical limits. More generally, we demonstrate that our mathematical analysis delivers physical insight that cannot be accessed through standard treatments.