We employ in situ deposited secondary membranes of yeast (SMYs) to optimize permeate flux during microfiltration and ultrafiltration of protein solutions. The deposited secondary membrane was periodically removed by backflushing, and a new cake layer was deposited at the start of the next cycle. The effects of backflushing time, backflushing strength, wall shear rate, and amount of secondary membrane deposited on the permeate flux were examined. Secondary membranes were found to increase the permeate flux in microfiltration by severalfold. Protein transmission was also enhanced owing to the presence of the secondary membrane, and the amount of protein recovered was more than twice that obtained during filtration of protein-only solutions under otherwise identical conditions. In ultrafiltration, the flux enhancement owing to the secondary membrane was only 50% or less. In addition, the flux for ultrafiltration was relatively insensitive to changes in the concentration of yeast used during deposition of SMY and to the backflushing strength used to periodically remove the secondary membrane.