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Soil quality plays a key role in sustainable agricultural productivity, particularly in semi-arid regions where fertility constraints limit crop performance. Microbial biofertilizers represent environmentally friendly alternatives to chemical fertilizers by enhancing nutrient availability and soil health. This study evaluated the effects of Bacillus subtilis and Aspergillus niger inoculations on the physicochemical properties of agricultural soils from the Béni Mellal region of Morocco. A total of 84 soil samples were analyzed, divided into four groups: untreated control, inoculated with B. subtilis, inoculated with A. niger, and combined inoculated. The results showed distinct treatment-dependent responses. B. subtilis significantly enhanced total nitrogen (N), while A. niger increased available phosphorus (P2O5) and influenced soil pH. Combined inoculation produced the most pronounced improvements, particularly for total nitrogen, available phosphorus, ammonium, and boron. Manganese (Mn) exhibited moderate but consistent variation among treatments, while organic matter (OM), carbon dioxide (CO2), iron (Fe), copper (Cu), and zinc (Zn) showed no significant short-term changes. Correlation analysis indicated strong positive associations among key nutrients, suggesting synergistic effects of microbial inoculation. Overall, the findings highlight the potential of Bacillus subtilis and Aspergillus niger, especially when combined, to selectively improve soil fertility and support more sustainable agricultural practices in the Beni Mellal region.