Proteases are enzymes that hydrolyze other proteins, including other proteases, which challenges assumptions of enzyme inertness in chemical reactions, and alters predicted protease−substrate concentrations using established mass action frameworks. Cysteine cathepsins are powerful proteases involved in numerous diseases by cleaving substrates, but they also hydrolyze each other, requiring inclusion of as yet undefined, protease-as-substrate dynamics. Here, we used experimental and computational models to improve predictions of the concentrations of multiple species and intermediates generated during substrate degradation in multiprotease systems by including protease-on-protease reactions of autodigestion, inactivation, cannibalism, and distraction in proteolytic networks. This was made available online for others to test perturbations and predict shifts in proteolytic network reactions and system dynamics (https://plattlab.shinyapps.io/catKLS/).