Recombinant Escherichia coli (E. coli) cells were successfully encapsulated in reactive membranes comprised of electrospun nanofibers that have biocompatible polyvinyl alcohol (PVA)-based cores entrapping the E. coli and silica-based, mechanically sturdy porous shells. The reactive membranes were produced in a continuous fashion using a coaxial electrospinning system coupled to a microfluidic timer that mixed and regulated the reaction time of the silica precursor and the PVA solution streams. A factorial design method was employed to investigate the effects of the three critical design parameters of the system (the flow rate of the core solution, protrusion of the core needle, and the viscosity of the core solution) and to optimize these parameters for reproducibly and continuously producing high-quality core/shell nanofibers. The feasibility of using the reactive membranes manufactured in this fashion for bioremediation of atrazine, a herbicide, was also investigated. The atrazine degradation rate (0.24 µmol/g of E. coli/min) of the encapsulated E. coli cells expressing the atrazine-dechlorinating enzyme AtzA was measured to be relatively close to that measured with the free cells in solution (0.64 µmol/g of E. coli/min). We show here that the low cost, high flexibility, water insolubility, and high degradation efficiency of the bioreactive membranes manufactured with electrospinning makes it feasible for their wide-spread use in industrial scale bioremediation of contaminated waters. Biotechnol. Bioeng. 2014;111: 1483–1493. © 2014 Wiley Periodicals, Inc.