In this study, organic matter degradation and microbial diversity were assessed during the composting of lignocellulose-rich digestates. Digestates were collected based on each crop type during anaerobic co-digestion of cow manure and barley, triticale, wheat and rye. Bacterial and fungal diversity in digestate composting systems were determined by 16S and 18S rRNA gene amplicon sequencing, respectively. Crop-based composting of anaerobic digestates showed similar process trends in terms of pH, temperature, moisture content (MC) and C:N ratio. The properties of final compost products were in accordance with the national legislations regarding soil applications, except MC, which were therefore air-dried before being amended to soil. Most abundant bacterial genera were represented by Luteimonas, Bacillus, Ochrobactrum and Thermobifida. Meanwhile, Thermomyces, Aspergillus, Galactomyces and Neurospora were detected as the predominant fungal genera in all compost samples.