This research evaluated the effect of the organic loading rate (OLR, g total solids (TS)/kg.d) at two temperature regimes on hydrogen productivity via consolidated bioprocess (CBP) of raw wheat straw in reactors operated in semicontinuous mode. The OLR from 6.0 to 20.0 g-TS/kg.d and from 4.0 to 30.0 g-TS/kg.d were assessed at 37 and 55 °C, respectively. The inoculum consisted of the native microbiota of the raw wheat straw. Results demonstrated that the temperature regime defined the biochemical routes for hydrogen production while the OLR influenced the abundance of hydrogen producers and productivities (p < 0.05). At 37 °C, the native microbiota produced hydrogen since the start-up of bioreactors, and an increase in the OLR resulted in the higher abundances of Lactobacillus and the fungus Pichia. The highest hydrogen productivity of 100 ± 11 mL/kg.d was reached at an OLR of 15.0 g-TS/kg.d with butyric and acetic acids as the main metabolites. At 55 °C, the native microbiota required 39 days to produce hydrogen, and an increase in the OLR favored the abundances of Clostridium, Thermoanaerobacterium, and the fungi Pichia and Cladosporium. The highest hydrogen productivity of 117 ± 31 mL/kg.d was reached at an OLR of 10.0 g-TS/kg.d with lactic acid as the main metabolite. This study demonstrated that after acclimation, the native microbiota produced hydrogen from the CBP of lignocellulose through two biochemical routes where the thermophilic operation improved substrate conversion by a factor of 1.7.