Background Microbial electrolysis is a promising technology for converting aqueous wastes into hydrogen. Substrate adaptability is an important feature, seldom documented in Microbial Electrolysis Cells (MECs). The correlation between substrate composition and community structure has not been well established. This study used a MEC capable of producing over 10 L/L-day of hydrogen from a switchgrass-derived bio-oil aqueous phase and investigated four additional substrates. The additional substrates included a red oak-derived bio-oil aqueous phase, a corn stover fermentation product, a mixture of phenol and acetate, and acetate alone. Results The MEC fed with the corn stover fermentation product resulted in the highest performance among the complex feedstocks, producing an average current density of 7.3 A/m2, although the acetate fed MEC outperformed complex substrates, producing 12 ± A/m2. 16S rRNA gene sequencing showed that community structure and community diversity were not predictive of performance, and replicate community structures diverged despite identical inoculum and enrichment procedure. The trends in each replicate, however, were indicative of the influence of the substrates. Geobacter was the most dominant genus across most of the samples tested, but its abundance did not correlate strongly to current density. High-performance liquid chromatography (HPLC) showed that acetate accumulated during open-circuit conditions when MECs were fed with complex feedstocks and was quickly degraded once closed-circuit conditions were applied. The largest net acetic acid removal rate occurred when MECs were fed with red oak bio-oil aqueous phase, consuming 2.93 ± 0.00 g/L-day. Principal component analysis found that MEC performance metrics such as current density, hydrogen productivity, and COD removal were closely correlated. Net acetic acid removal was also found to correlate with performance. However, no bacterial genus correlated to performance metrics, and the analysis suggested that less than 70% of the variance was accounted for by the two components. Conclusions This study demonstrates the robustness of microbial communities to adapt to a range of feedstocks and conditions without relying on specific species, delivering high hydrogen productivities, thus indicating functional adaptation vs. compositional requirement. MECs may,, play a central role in the 21st-century bioeconomy as factories producing a zero-emission fuel.