A micro-bioelectrochemical cell (μ-BEC) device is disclosed that includes from 4 to 96 microfluidically connected of chambers, in which each chamber encloses a volume of about 1 μL to 2 μL. A working electrode, reference electrode, and counting electrode contacts each volume. The μ-BEC device includes a support layer coated with a working electrode layer, a microfluidics layer containing a plurality of wells, and an electrical layer containing the reference and counter electrodes. Methods of using the μ-BEC device to perform bioelectrochemical measurements of cells are also disclosed.