Pulsed electric field (PEF) processing of juice has been intensively studied with benchtop scale experiments. However, there is still limited information regarding critical factors to be considered for PEF efficacy in microbial reduction with PEF processing during pilot or commercial scale production of juice. In the present study, continuous benchtop (3.6–7.2L/h) PEF processing systems with co-field treatment chambers and bipolar square waveform pulses were used and simulated production conditions were tested for pomegranate juice. Microbial reductions of Escherichia coli, as affected by PEF process conditions (field strength, pulse width, pulse frequency, total treatment time, input energy), production conditions (flow rate, juice holding time and temperature), and juice properties (pH, conductivity, particulate), were investigated. Flow rate, PEF process parameters, production conditions, type of target microorganism, and properties of juice significantly affected microbial reductions by PEF treatments. E. coli ATCC 35218, a non pathogenic surrogate bacterium, exhibited higher resistance to PEF treatments than E. coli O157:H7 and E. coli K12 in pomegranate juice. Increase of a single PEF parameter (field strength, pulse width, pulse frequency, total treatment time, or energy input) is insufficient to achieve maximum microbial reduction. Optimal PEF treatment conditions for maximum microbial reduction depend on multiple factors including PEF processing parameters, production conditions and product properties. This study demonstrates that scale-up and validation studies in a specific PEF system for specific products are very important and necessary before successful commercial application of this novel technology is possible.