The aim of this work was to study the cleaning of inorganic membranes fouled with whey protein solutions using the enzymatic formulation Alcalase (Novo Nordisk A/S). Hydraulic and chemical methods were considered to characterize the cleanliness of the membranes. Cleaning efficiency was observed to be a function of the operating conditions. The operating conditions tested were the following: recycling versus non-recycling of permeate, pH of the cleaning solution, addition of alkali to regulate the pH, enzymatic agent concentration, and cleaning time. The best conditions to perform the cleaning were related to the best conditions to hydrolyze whey proteins in a discontinuous reactor using the same enzyme preparations. Very high cleaning efficiencies (>90%) were achieved in short operating times (20 min). However, residual matter was observed on the membrane surface.