Data in this article provide detailed information on the microbial dynamics during inhibition of anaerobic digestion by phenol and ammonia. Ten concentrations of both inhibitors were tested in triplicates. Data include the operational conditions and degradation performance measurements, as well as microbial community analysis, by 16S rRNA gene sequencing, at different time points for the different conditions (96 samples). Sequencing data were generated by using IonTorrent PGM sequencer. This data is associated with the research articles “Community shifts within anaerobic digestion microbiota facing phenol inhibition: Towards early warning microbial indicators?” (Poirier et al., 2016a) [1] and “Anaerobic digestion of biowaste under extreme ammonia concentration: Identification of key microbial phylotypes” (Poirier et al., 2016b) [2]. The sequencing data have been deposited in the bioproject PRJNA450311, with the dataset identifier (TaxID) 1263854. Samples accession numbers go from SAMN08934853 to SAMN08934947.