The performance of a demonstration-scale anaerobic reactor treating food waste was evaluated with an emphasis on microbial response to increasing organic loading rates (OLRs). The reactor exhibited a stable performance in terms of methane yield at OLR ranging from 1.0 to 2.4 kg VS L−1 day−1 (phases I and II), compared to that at phase III (OLR: 1.0–1.5 kg VS L−1 day−1) when the food waste exhibited greater acidity. Deep sequencing analysis revealed shifts in the microbial composition at each operational phase. The phyla Firmicutes and Bacteroidetes were favoured, whereas the abundance of Proteobacteria and Chloroflexi decreased at higher OLRs, indicating that fermenting-, hydrolytic- (and acidogenic) bacteria were selected under this condition. Changes were observed in the composition of methanogens, and not the abundance, in response to a shift in OLR. Methanosaeta and Methanospirillum dominated at low OLRs, indicating the importance of both acetoclastic and hydrogenotrophic methanogens for methane production during this condition. Methanosaeta almost disappeared at high OLRs, whereas Methanoculleus was favoured. Syntrophic prokaryotes were in high abundance (>9%), indicating that syntrophic methane production was important in this reactor. Syntrophic interactions between hydrogen-producer (Syntrophomonas and Desulfosporosinus) and hydrogenotrophic methanogens were more evident at high OLR. These results indicate that hydrogenotrophic methanogenesis contributed significantly to methane production at higher OLRs than when the reactor was operated at low OLR.