End-product accumulation during dark fermentation leads to process instability and hydrogen production inhibition. To overcome this constraint, microbial community adaptation to butyric acid can induce acid tolerance and thus enhance the hydrogen yields; however, adaptation and selection of appropriate microbial communities remains uncertain when dealing with complex substrates in a continuous fermentation mode. To address this question, a reactor fed in continuous mode with food waste (organic loading rate of 60 gVS·L·d−1; 12 h hydraulic retention time) was first stressed for 48 h with increasing concentrations of butyric acid (up to 8.7 g·L−1). Performances were compared with a control reactor (unstressed) for 13 days. During 6 days in a steady-state, the pre-stressed reactor produced 2.2 ± 0.2 LH2·L·d−1, which was 48% higher than in the control reactor (1.5 ± 0.2 LH2·L·d−1). The pretreatment also affected the metabolites’ distribution. The pre-stressed reactor presented a higher production of butyric acid (+44%) achieving up to 3.8 ± 0.3 g·L−1, a lower production of lactic acid (−56%), and an enhancement of substrate conversion (+9%). The performance improvement was attributed to the promotion of Clostridium guangxiense, a hydrogen -producer, with a relative abundance increasing from 22% in the unstressed reactor to 52% in the stressed reactor.