The invention relates to a method for treating an influent stream comprising a digestible waste, the method comprising filtering a mixed liquor in the membrane bioreactor, wherein the mixed liquor is contacted with outer surfaces of a plurality of porous hollow fiber membranes, and wherein a permeate is removed from lumens of the membranes, removing biological solids from the membrane bioreactor by recycling a substrate containing biological solids to an offline treatment vessel via a recycle loop, whereby a preselected concentration of biological solids is maintained within the membrane bioreactor, digesting biological solids in the offline treatment vessel, and conducting an effluent stream from the offline treatment vessel to the membrane bioreactor, wherein the effluent stream comprises at least a portion of the mixed liquor.