In this study, the effect of pre-treatments including alkaline, acid and hydrogen peroxide on continuous hydrogen and methane production was investigated. Two different substrates as potatoes and bean wastes were used. Pre-treatment showed positive effect on bio-hydrogen and bio-methane production; higher bio-hydrogen and bio-methane production results using pre-treated samples than the control bioreactors (without pre-treatment), were recorded. In case of potatoes wastes, the hydrogen yield ranged between 126.4 and 252.7 mL-H-2/gTVS using pre-treated samples compared to 58.7 mL-H-2/gTVS observed in the reference test. Pre-treated bean wastes showed hydrogen yield of 93.0-152.1 mL-H-2/g-TVS higher than 53.3 mL-H-2/g-TVS measured in the control test. In the second stage, average methane yield results of 322.9-507.1 and 284.3-462.6 mL-CH4/g-TVS higher than 198.6 and 124.3 mL-CH4/g-TVS measured for potatoes and bean wastes control bioreactors, respectively. The best results were observed using H2O2 pre-treatment. The energy production efficiency was improved by combining H-2 and CH4 bioreactors.