BACKGROUND The uncontrolled overproduction of fruit and vegetable waste causes serious environmental challenges such as emission of greenhouse gases. Anaerobic digestion (AD) is becoming a widely adopted technology for treatment of food waste with the concomitant production of biogas. This study investigated the link between microbial community structure and biogas production when using cow dung and mixed fruit and vegetable waste (MFVW) as substrates. RESULTS Semi-continuous stir tank reactors were used for AD of cow dung and MFVW over a period of 40 days. The highest accumulative methane yield (112.9 L) was obtained from co- digestion, intermediate yield (59.5 L) was obtained from cow dung and lowest yield (6.1 L) from MFVW at the end of the digestion experiment. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) revealed higher bacterial and archaeal diversity indices in co-digestion in comparison to mono-digestion of cow dung and MFVW. High-throughput sequence analyses showed that operational taxonomic units (OTUs) belonging to the phyla Bacteroidetes, followed by Firmicutes, Actinobacteria and Proteobacteria were dominant in all treatments. CONCLUSION The results of the study demonstrated that the enhanced methane production in co-digestion could be attributed to the neutral pH and partial shift of archaea from Methanosaeta to Methanosarcina rich communities. (c) 2019 Society of Chemical Industry