Acidogenic fermentation is an anaerobic process of double purpose, while treating organic residues it produces chemical compounds, such as hydrogen, ethanol and organic acids. Therefore, acidogenic fermentation arises as an attractive biotechnology process towards the biorefinery concept. Moreover, this process does not need sterile operating conditions and works under a wide range of pH. Changes of operating conditions produce metabolic shifts, inducing variability on acidogenic product yield. To induce those changes, experiments, based on reactor headspace N(2)-flushing (gas phase), were designed. A major result was the hydrogen yield increase from 1 to 3.25±0.4 ( [Formula: see text] ) at pH 4.5 and N(2)-flushing of 58.4 (L·d(-1)). This yield is close to the theoretical acidogenic value (4 [Formula: see text] ). The mechanisms that explain this increase on hydrogen yield shifts are related to the thermodynamics of three metabolic reactions: lactate hydrogenase, NADH hydrogenase and homoacetogenesis, which are affected by the low hydrogen partial pressures.