A method and system for the production of valuable chemicals or alternative liquid fuels via an integrated biomass conversion and upgrading process is disclosed. The process integrates three subcomponent processes, capturing the desirable attributes of each: zoned partial oxidation, alcohol production, and gas-to-liquids reformation. The method and system may include reacting gasification intermediates—e.g., syngas from zoned partial oxidation, with bioprocessing intermediates—e.g., aqueous ethanol from alcohol production in a reactive separation to produce a product(s) of higher alcohols, liquid hydrocarbons, or a combination of these. The product(s) can be split into two (or more) boiling point fractions by the same reactive separations unit operation. The resulting product(s) are valuable for a variety of applications, including potentially as alternative (non-fossil-based) liquid transportation fuels.