Mechanochemical treatment of various organic molecules is an emerging technology of green processes in biofuel, fine chemicals, or food production. Many biopolymers are involved in isolating, derivating, or modifying molecules of natural origin. Mechanochemistry provides a powerful tool to achieve these goals, but the unintentional modification of biopolymers by mechanochemical manipulation is not always obvious or even detectable. Although modeling molecular changes caused by mechanical stresses in cavitation and grinding processes is feasible in small model compounds, simulation of extrusion processes primarily relies on phenomenological approaches that allow only tool- and material-specific conclusions. The development of analytical and computational techniques allows for the inline and real-time control of parameters in various mechanochemical processes. Using artificial intelligence to analyze process parameters and product characteristics can significantly improve production optimization. We aim to review the processes and consequences of possible chemical, physicochemical, and structural changes.