The effect of heat-shock treatment to selectively enrich acidogenic, H2 producing consortia was investigated for inoculum preparation and to control the process operation. Long term operation (520 days) in suspended-batch mode bioreactors illustrated relative efficiency and feasibility of heat-shock treated consortia (15.78 mol/kg CODR) in enhancing H2 production (3.31 mol/kg CODR) when compared to parent (control) consortia. On the contrary, substrate degradation was higher in the control operation (ξCOD, 62.86%; substrate degradation rate (SDR), 1.34 kg CODR/m3-day) compared to heat-shock operation (ξCOD, 52.6%; SDR, 1.10 kg CODR/m3-day). Heat-shock pretreatment has resulted in a marked fermentation pathway shift towards acetic-butyric acid type production. The microbial diversity illustrated dominance in the Clostridia class after applying heat-shock pretreatment. The redox catalytic currents and Tafel analysis strongly support the conclusion of an improved biocatalyst performance after pretreatment with regards to H2 production.