The aim of this study is to highlight the robustness and potentials of the anaerobic baffled reactor (ABR) configuration on keeping the microbial richness and diversity after starvation period of 7 days. The module at steady state operating conditions provided an average volumetric hydrogen production (VHP) of 0.2 +/- 0.08 and 0.423 +/- 0.5 l/d in the 1st and last compartment (C4). The VHP was gradually decreased from 0.2 to 0.003 l/d and from 0.423 to 0.1 l/d in compartments (C1 and C4) respectively during feed less period. However, the VHP was substantially increased up to 0.035 and 0.152 l/d in 1st (C1) and fourth compartment (C4) within 24 h, after reoperation of the ABR. Moreover, the H-2 producers of Clostridiaceae, Ruminococcaceae, and Enterobacteriaceae families were dominant in the reactor after reoperation process. Quantitative polymerase chain reaction and next-generation sequencing methods results revealed that the microbial community structure was mainly composed of Proteobacteria, Firmicutes, Chloroflexi, Bacteroidetes, Planctomycetes, and Actinobacteria. The results showed the unique properties of the ABR configuration for keeping the microbial richness and diversity during feed less period.