This paper reviews and discusses the impact of byproducts released during pretreatment of lignocellulosic materials on anaerobic mixed cultures producing hydrogen and methane. 5-HMF, furfural, phenolic compounds and aldehydes, are strong inhibitors of biohydrogen production but can be further converted into methane. This finding can be explained by differences in both process parameters: anaerobic digestion is performed with more complex mixed cultures, lower substrate/inoculum or byproducts/inoculum ratios and longer batch incubation times than dark fermentation. Indeed, the presence of byproducts may require an adaptation phase of the microbial community leading to longer lag phase in dark fermentation. Finally, the presence of pretreatment by-products may lead to a metabolic shift from hydrogen production to no H2-producing ethanol and lactate pathways and whatever the route of dark fermentation, metabolites can be all further converted into methane, at different rates.