Electrochemical hydrogenation is gaining increasing attention due to its ability to selectively convert desired functionalities within organic species without the need to manipulate temperature or pressure as it is typically done for thermocatalytic processes. Instead, the driving force for the reaction is the applied potential. This technology is especially desired for biomass conversion reactions as many biobased products are sensitive to elevated temperatures and undergo undesired side reactions. Electrochemical hydrogenation is also desired for the upgrading of biologically-produced platform chemicals due to incompatibilities between fermentation media and conventional heterogeneous catalysts. Our prior work showed that by using electrochemical hydrogenation, we can selectively convert biologically-produced muconic acid (MA) to trans-3-hexenedioic acid (t3HDA) directly in the fermentation broth. We also demonstrated that t3HDA can be functionalized and then introduced into a nylon 6,6 structure to confer desired physical or chemical properties to the polymer at a cost comparable to that of adipic acid. Building on our previews work, we translate here the electrohydrogenation process from a small-volume batch reactor to a benchscale flow reactor for continuous operation. We also demonstrate the use of a bismuth electrode rather than a lead electrode in order to remove the potential of toxic byproducts known to occur from lead leaching. By utilizing linear sweep voltammetry (LSV), cyclic voltammetry (CV) and then conducting bulk electrolysis on a looped flow reactor, we were able to show that the bismuth electrode had a very similar performance to that of lead without the need of a potentially toxic metal. Finally, we were able to demonstrate an increase in the productivity of t3HDA of over 50 times compared to our previews work.