Data in this article provide detailed information on the microbial dynamics within digesters supplemented with different support media (two types of zeolites, two types of activated carbons, one type of chitosan, one control) in presence of different inhibitory conditions (control without inhibitor, 1.3 g/L of phenol and 19 g/L of total ammonia nitrogen). 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 (samples). Sequencing data were generated by using IonTorrent PGM sequencer. This data is associated with the research articles “Improving anaerobic digestion with support media: Mitigation of ammonia inhibition and effect on microbial communities?” (Poirier et al., 2017) [1] and “Support media can steer methanogenesis in presence of phenol through biotic and abiotic effects” (Poirier et al., 2018) [2]. The sequencing data have been deposited with links to BioProject accession number PRJNA450513, in the NCBI BioProject database (https://www.ncbi.nlm.nih.gov/sra/?term¼ PRJNA450513). Samples accession numbers go from SAMN08940368 to SAMN08940426