The aim of the present paper is the improvement of dark fermentative hydrogen production from problematic substrates. In detail, the study is aimed at (i) investigating the inhibiting effect of two problematic biomasses (i.e., of olive mill wastewater, containing recalcitrant/toxic compounds and cheese whey, lacking pH buffering capacity) on the dark fermentation process, (ii) as well as verifying the possibility to apply a co-fermentation strategy to enhance the process. To investigate the inhibiting effect of the substrates, two experimental sets were conducted using olive mill wastewater and cheese whey alone, under different food-to-microorganism ratios (i.e., 1, 2.5, and 5). Further experiments were conducted to verify the possibility of improving hydrogen production via the co-fermentation strategy. Such experiments included two tests conducted using different volumetric percentages of olive mill wastewater and cheese whey (90% olive mill wastewater + 10% cheese whey and 80% olive mill wastewater + 20% cheese whey). Results show that using olive mill wastewater alone, the inhibiting effect increased at a higher food-to-microorganism ratio. Moreover, because of the occurrence of a metabolic shift, hydrogen was not produced using 100% cheese whey. Interestingly, compared to the 100% olive mill wastewater condition, the use of 20% cheese whey allowed to double the hydrogen yield, reaching the high cumulative hydrogen production of 2.08 LL−1. Obtained results confirm that the two investigated substrates exert inhibiting effects on microorganisms. Nevertheless, co-fermentation is an effective strategy to improve the dark fermentation process of problematic biomass.