In the present paper we discuss different aspects of the soil biota functioning in the current farming system of the Republic of Moldova. The natural stability of the biota in virgin, fallow and arable soils has been estimated, the assessment system of the sustainability of invertebrates and microorganisms of soils to the anthropogenic impacts has been developed. The zones of homeostasis have been determined and criteria of the resistance of soil biota standards have been elaborated. The modifications of the biological properties of soils have been established, as a result of their long-term arable use and the application of high doses of mineral fertilizers. More information about the biological soil degradation has been acquired, as a result of dehumification processes and aggregates destroying the anthropogenic nature. The system of fertilizers application on soils with a normal profile has been substantiated from the biological point of view. The method of green manure application has been applied in order to restore the biota of degraded soils and to improve soil quality and the environment.