A method and system for the enzymatic treatment of a lipid containing feedstock comprises contacting the feedstock with a processing aid, then causing the feedstock to pass at a substantially constant flow rate through a treatment system comprising a plurality of enzyme-containing fixed bed reactors connected to one another in series. The fixed bed reactors can be individually serviceable, the flow rate of the feedstock remaining substantially constant through the system when one of the fixed bed reactors is taken off line for servicing. In the most preferred embodiment, the processing aid is a substantially moisture-free silica. The processing aid can be placed in one or more of the fixed bed reactors, disposed above the enzyme in the reactor, or it can be in a pre-treatment system which can comprise one or more reactors.