The presence of poorly biodegradable components in lignocellulosic biomass limits the methane recovery in anaerobic digesters. The main reason to go for aerobic pretreatment before anaerobic digestion (AD) is to enable enzymatic cleavage of the aromatic rings in lignin by oxygen since it cannot be efficiently degraded under anaerobic conditions. In this study, the advantage of highly-cellulolytic white-rot fungi Trametes versicolor was taken by aerobic pretreatment prior to anaerobic co-digestion of cow manure and selected cereal crop materials (i.e. wheat, rye, barley, triticale) harvested at different stages. Fungal pretreatment improved the methane yield by 10%-18% and cellulose degradation up to 80%. Furthermore, higher volatile fatty acid (VFA) speciation was found in the anaerobic digesters upon fungal pretreatment. 16S rRNA gene amplicon sequencing revealed a more diverse microbial community in the fungal-pretreated anaerobic digesters. Generally, typically-detected bacterial species dominated the digesters; except that Synergistetes was only enriched in the fungal-pretreated digesters. Although Methanosarcianease was the predominant methanogenic archaea, a more diverse methanogenic population was identified in the fungal-pretreated digesters in which Methanobacteriaceaa and Methanomibrobiaceae also took role during biomethanation. Comparatively more unique microbiome of biogas reactors upon fungal pretreatment synergistically affected VFA production, cellulose degradation and eventually methane yield in an affirmative way. Considering the functional importance of bacterial and methanogenic archaeal populations, elevated knowledge of the microbial structures is essential for minimizing process failures and for creating strategies for process optimization of lignocellulose based-AD.