Microbial bioelectrochemical systems (BESs) use microorganisms as catalysts for electrode reactions. They have emerging applications in bioenergy, bioproduction, and bioremediation. BESs can be scaled up as a linked series of units or cells; however, this may lead to so-called cell reversal. Here, we demonstrate a cell balance system (CBS) that controls individual BES cells connected electrically in series by dynamically adapting the applied potential in the kilohertz frequency range relative to the performance of the bioanode. The CBS maintains the cell voltage of individual BES cells at or below a maximum set point by bypassing a portion of applied current with a high-frequency metal oxide semiconductor field-effect transistor switch control system. We demonstrate (i) multiple serially connected BES cells started simultaneously and rapidly from a single power source, as the CBS imparts no current limitation, (ii) continuous, stable, and independent performance of each stacked BES cell, and (iii) stable BES cell and stack performance under excessive applied currents. This control system has applications for not only serially stacked BESs in scaled-up stacks but also rapidly starting individual- and/or lab-scale BESs.