Proper management of soil organic matter in arid and semi-arid regions improves organic carbon storage in the soil, helps in compact soil degradation, mitigates climate change impacts, and preserves ecosystem functionality and sustainability food security. This study aims to provide a better insight into the biogeochemical processes that drive the organic carbon dynamics of saline clay soil in a semi-arid area. The study is not intended to be exhaustive but contributes to analyzing the relationship between bacterial microflora, physicochemical properties, and organic carbon dynamics as a function of different soil management modes. The monitoring was carried out on three different plots located at the National Institute of Agronomic Research of Algeria. A physicochemical characterization of the soils was performed. A metagenomic study was also conducted to identify bacterial biodiversity using PCR-amplified DNA sequencing. The study results show that the control plot has the highest average organic carbon stock value at 47 Mg ha-1. This was followed by the amended plot and the conventional plot, respectively, with 43 Mg ha-1 and 38 Mg ha-1. In the context of this study, organic carbon dynamics would appear to depend on the interaction of several biotic and abiotic factors. Soil management methods would impact the density and diversity of bacterial microflora. This, in turn, affects the soil's physicochemical properties and, more specifically, organic carbon dynamics and storage.