The review article discusses the application of biogeochemical technologies aimed at restoring biogeochemical cycles in agroecosystems, primarily in the microbial link regulating CO<sub>2</sub> flows. The factors of management this microbial link when applying mineral and organic fertilizers are shown. The processes of mineralization of soil organic matter and methods of controlling soil's conjugate carbon- and nitrogen-mineralizing ability are considered. The changes in the productivity of agricultural ecosystems under conditions of increasing concentration of carbon dioxide in the atmosphere and soil air are considered. Various agrotechnological techniques are considered, including using zero tillage, organic fertilizers of various nature, and various meliorants, including phosphogypsum. Examples of recultivation of disturbed and polluted soils, waterlogged and/or over-drained soils are given and the impact on CO<sub>2</sub> fluxes is estimated. Based on numerous data, it is concluded that agroecosystems in most cases are a net source of CO<sub>2</sub>, and sequestration occurs only when agricultural land is transferred to fallow lands and at afforestation. At the same time, techniques aimed at reducing CO<sub>2</sub> fluxes using fertilizers in the "production–application" cycle are evaluated. A set of biogeochemical technologies aimed at assessing and stabilizing the microbial link of the biogeochemical cycle in agroecosystems is presented. Examples of the use of these technologies for regulating CO<sub>2</sub> emissions in agroecosystems are given. Using one of the biogeochemical technologies, the almost 5-fold decrease in the rate of CO<sub>2</sub> flows during the reclamation of disturbed tundra ecosystems is shown. Adopting agricultural low carbon technologies (ALCTs) cannot yet testify to their applicability to ensure both food and environmental safety. It is necessary to further develop and use biogeochemical technologies to restore biogeochemical cycles in agroecosystems, primarily in the microbial link regulating CO<sub>2</sub> flows.