Abstract <p>Quantitative characteristics of soil biota—numbers of gene copies of microorganisms, abundance and diversity of culturable bacteria and fungi, and the diversity and abundance of earthworms—were studied in cultivated soddy-podzolic soils (Retisols) of Tver region for variants with different crops in the presence/absence of fertilizers and drainage. The abundance of microorganisms was determined by counting colony-forming units on different nutrient media; earthworms were counted by manually sorting soil samples. The application of mineral fertilizers had a positive effect on the numbers of ammonifiers, actinomycetes, fungi, and denitrifiers, but reduced the abundance of amylolytic bacteria. It also contributed to an increase in the numbers and activity of soil denitrifiers. Closed drainage favored some increase in the numbers of ammonifiers, micromycetes, actinomycetes, and the biomass of earthworms. Wheat cultivation with clover understory increased the numbers of amylolytic bacteria, actinomycetes, and earthworms. None of the studied factors had a significant effect on the copy numbers of archaea and bacteria genes. The diversity of amylolytic and oligotrophic actinomycete morphotypes, as well as the biomass of earthworms, proved to be the most sensitive indicators of changes in the biological state of soddy-podzolic soils during their agricultural use. The data obtained indicate the multidirectional influence of agrogenic factors on the biological characteristics of soddy-podzolic soils highlighting the need for an integrated approach to assessing their condition when planning farming techniques.</p>