This study evaluated a new automated system using alternative irrigants for root canal cleaning treatments. This method relies on a system inserting an enzymatic solution based on Trypsin flowing inside the pulp chambers and root canals, completely avoiding traditional endodontic instrumentation. Sixty freshly extracted human molar teeth were randomly divided into 4 groups to assess 3 regimens (R1-3) differing in 0.25% Trypsin/EDTA and 5% Sodium Hypochlorite (NaOCl) solutions administration. Scanning electron microscopy observations and scores taking into account changes in dentin tubules were used to assess treatment effects in pulp chambers and roots. Significant changes in root cleaning ability relative to administration timing were observed, with the best results found in R3, with scheduled alternated cycles of Trypsin/EDTA and NaOCl inside the tooth. The non-invasive root canal method demonstrates good teeth cleaning ability independent of root morphology. This equipment may provide lower discomfort levels for patients undergoing endodontic treatment.