The purpose of the study was to link microbial community composition and chemical properties of various biomass and their resulting digestate residues for their potential use in biogas production or soil enrichment. The order of biogas production, graded from high to low was as follows: corn silage, grass silage, fruit waste, and dairy sewage sludge. Different bacterial families were predominant in different biomass. Corn silage deteriorated as a result of long-term air exposition and may serve as an efficient feedstock substrate for anaerobic digestion. A positive role in plant biocontrol microorganisms found in grass straw residues, and reasonable biogas yield obtained from this substrate suggests the use of grass straw for biogas production and its residues to enrich the soil. Due to potential threat of introducing pathogens into the soil within fruit waste or dairy sewage sludge, or soil acidification by fruit waste repeated use in field application, this biomass should be sanitized prior to soil application. Simultaneously, low biogas yields from fruit waste and dairy sewage sludge substrates make it necessary to transform them in anaerobic digestion with more energetic co-substrates. Tested residues may deliver a robust and wide range of methanogens as inoculum for further anaerobic digestion process.