The quality of an inoculum has a considerable impact on the performance of a biogas reactor. The aim of this study was to investigate the effect of storing inoculum under different conditions. Inoculum from a biogas plant running on food waste and cow manure was stored at room temperature (RT), 4oC and -20oC for 1 week, 1, 2, 6 and 11 months in batch bottles. Cellulose was then added as a standard substrate for anaerobic digestion during a time-course of 40 days. Taxonomic profiling of the microbial community (bacteria and archaea) in all batch reactors were analyzed using 454 pyrosequencing of 16S rRNA gene sequences.