Stirred cell microfiltration of industrial relevant enzyme solutions, with and without cell debris, was studied. The biological system used was a recombinant intracellular cutinase in suspensions of Escherichia coli fragments. In NaCl solutions, cutinase forms large soluble protein aggregates that vary in size with the electrostatic microenvironment. Filtration shear forces applied on these aggregates break the interaction among monomers, allowing 100% transmission of cutinase to permeate. Pure enzyme solutions showed permeation flux reduction (10-34% of simple electrolyte filtration runs) caused by adsorption and aggregated protein molecules, leading to membrane fouling by formation of dynamic cake layers. Cell homogenates presented severe decrease on permeation flux (range of 93-97%), leading to similar flux values, still dependent on the colloidal microenvironment. The presence of cutinase led to cell debris concentration polarisation layers less resistant to flow. The experimental filtration results were evaluated in accordance to the aggregation behaviour of cutinase, average size of cell debris and zeta potential of the colloidal particles and of the membrane.