Research into the correlations among components of soil biota is of significant importance for effective management of agroecosystems in organic agricultural production. Organic cultivation technologies contribute to increased nitrogen and phosphorus content in the soil, while reducing levels of P2O5 and K2O compared to inorganic methods. The influence of organic residue decomposers on macroelement composition in the soil has been examined, revealing a minimal impact on their levels. Organic technologies promote an augmentation of microorganisms, although there is a potential risk of heightened disease pathogens. It has been observed that under organic cultivation conditions, there is more intense tissue degradation, potentially attributed to higher microorganism activity. Transitional cultivation methods yield lower rates of degradation in comparison to organic techniques. The impact of organic technologies on the quantity of earthworms, nematodes, and springtails in the soil has been investigated. Organic practices have shown to increase their population, creating a favorable environment for soil biological indicators. Particular attention is given to correlation relationships between microorganisms responsible for nitrogen and phosphorus accumulation and the fungal component. High correlation values (r = 0.72–0.89) underscore the significance of comprehending these associations when employing organic cultivation methods. The study of correlations among soil biota components in organic production presents a promising task for the effective utilization of resources and the assurance of sustainable agroecosystem development.