Sugars released by thermochemical pretreatment of lignocellulosic biomass are possible substrate for hydrogen production. However, the major drawback for bacterial fermentation is the toxicity of weak acids and furan derivatives normally present in such substrate. This study aimed to investigate the metabolism involved in hydrogen production by the isolate Enterobacter LBTM2 using 10, 20 and 30-fold diluted synthetic (SH) and sugarcane bagasse hemicellulose (SBH) hydrolysates. In addition, the effects of acetic acid, formic acid and furfural on the bacterial metabolism, as well as detoxification of SBH with activated carbon and molecularly imprinted polymers on the hydrogen production were assessed. The results showed the best hydrogen yield was 0.46 mmol H2/mmol sugar for 20-times diluted SH, which was 2.3-times higher than obtained in SBH experiments. Bacterial growth and hydrogen production were negatively affected by 0.8 g/L of acetic acid when added alone, but were totally inhibited when formic acid (0.4 g/L) and furfural (0.3 g/L) were also supplied. However the maximum hydrogen production of SBH20 has duplicated when 3% of powdered activated carbon was added to the SBH experiment. The results presented herein can be helpful in understanding the bottlenecks in biohydrogen production and could contribute towards development of lignocellulosic biorefinery.