The design and construction of continuous flow biochemical reactorscomprising immobilized biocatalysts have generated great interest in the efficient synthesis of value-added chemicals. Living cells use compartmentalization and reaction-diffusion processes for spatiotemporal regulation of biocatalytic reactions and implementing these strategies into continuous flow reactors could offer new opportunities in reactor design and application.Herein, we demonstrate the fabrication ofprotocell-based continuous flow reactors for enzyme and whole-cell mediated biocatalysis. We employ semipermeable membranized coacervate vesicles as model protocells that spontaneously sequester enzymes or accumulate living bacteria to produce embodied microreactors capable of single- or multiple-step catalytic reactions. By packing millions of the enzyme/bacteria-containing coacervate vesicles in a glass column, we demonstrate a facile, cost-effective, and modular methodology capable of performing oxidoreductase, peroxidase and lipolytic reactions, enzyme-mediated L-DOPA synthesis and whole-cell glycolysis under continuous flow conditions. We show that the protocell-nested enzymes and bacterial cellsexhibit enhanced activities and stability under deleterious operating conditions compared with their non-encapsulated counterparts. Our results provide a step towards the engineering of continuous flow reactors based on cell-like microscale agents and offer opportunities in the development of green and sustainable industrial bioprocessing. This article is protected by copyright. All rights reserved.