The growing global population and increasing demand for agricultural products have exerted significant pressure on agricultural systems. As a result, soil organic matter depletion and degradation have become prevalent issues, including in regions such as South Bohemia, Czech Republic, where conventional farming practices are predominant. Soil organic matter (SOM) plays a critical role in soil health, crop productivity, and the sustainability of agricultural systems, with changes occurring in both the total and labile fractions of the organic matter pools. However, changes in the total soil organic matter carbon pool (TOC) resulting from agricultural practices occur gradually and may become evident only after several years, posing challenges for timely management adjustments. Therefore, the identification of early indicators of SOM dynamics is crucial for implementing prompt corrective actions. The aim of this study was to evaluate the effects of sustainable management practices, such as cultivated crops (Pisum sativum and Lupinus albus), selected entomopathogenic and myco parasitic fungi (MEHA) (Trichoderma virens and Metarhizium brunneum), and lactic acid bacteria (LAB) on the labile fraction of the SOM pool (C_LSOM) and identify potential early indicators. Our findings demonstrated that the type of crop and applied microorganisms (treatments) significantly affected the C_LSOM in peas, and the crop growth stages affected the TOC in both pea and lupin. Growth stages also showed an impact on the C_LSOM in lupin. Moreover, in both crops, the change in C_LSOM correlated with changes in the SOM oxidation rate constant (k), carbon lability index (LI), carbon management index (CMI), and carbon enrichment ratio (ER). Conversely, changes in the TOC did not exhibit significant correlations, except for LI and CMI, which showed a positive correlation with the TOC in peas (p < 0.05). Furthermore, the separate application of MEHA and LAB on seeds or leaves resulted in increased SOM carbon pools compared with the combined application. The application of these beneficial microorganisms in pea and lupin crops showed potential in maintaining or increasing C_LSOM, which can be assessed early through indicators such as k, LI, CMI, and ER. Contributing to the development of sustainable soil management strategies, future research should further investigate different crops and microorganisms—and the mechanisms underlying their observed relationships—and explore additional early indicators to refine and optimize sustainable agricultural practices.

Organic matter has a very important function in soil, without which, soil formation processes cannot take place properly. It can be divided and classified based on several aspects; the most general division is between the living and non-living parts of organic matter. The results presented in this paper specifically refer to the living microbial part of organic matter. This research was carried out in the years 2021–2024 in the South Bohemia region located in the Czech Republic. Two types of land use (four permanent grassland areas, two forest areas) were evaluated. Based on laboratory soil analyses, some significant dependencies were found. For example, in grasslands with statistically identical pH, there was a dependence (p-value 0.05) between soil organic carbon (SOC), carbon of microbial biomass (MBC) and microbial basal respiration (MBR). Additionally, coniferous forest experimental locations had a lower pH, which, in turn, slowed the activity of microorganisms and promoted the accumulation of SOC in the soil. The results from this experiment support the current knowledge of organic matter and are important for a better understanding of the soil organic matter cycle.