Plant residues are the main source of humus and some nutrients in soils. The composting of organic waste using modifiers is a promising way to obtain high-quality organic fertilizers. Here, the effect of biochar and calcium carbonate on the abundance and taxonomic composition of bacteria and fungi in mature plant compost has been studied using metagenomic analysis. Plant materials with different initial C:N ratios—low (22, clover), medium (38, rye) and high (68, oats)—served as composting materials in the pot experiment. The plant material mixed with sterile sand was modified by the addition of biochar or calcium carbonate. Both ameliorants increased pH values and humic acid content in composts irrespective of plant material composition. Representatives of the phyla Proteobacteria, Actinobacteriota and Firmicutes dominated among bacteria and representatives of the division Ascomycota dominated among fungi in the mature composts, as in the initial plant samples. The abundances of bacteria and fungi in the cereal composts were higher than in the composts with clover. The effect of biochar and calcium carbonate on the number and taxonomic composition of bacteria and fungi in composts from the same plant material was similar, while the effect of reagents in composts from different raw materials was ambiguous. No one dominant group of bacteria was found to develop in response to biochar or calcium carbonate application in any of the types of composts studied. However, the structure of the fungal community both at the phylum and genus levels changed significantly under the influence of these additives. The addition of calcium carbonate and biochar led to an increase in the abundance of the same groups of fungi, but this increase was different for composts made from different plant materials.