Excessive use of nitrogen fertilizers can alter soil nitrogen fractions and physicochemical properties. This study aimed to evaluate changes in nitrogen fractions and physicochemical properties of agricultural soil following the application of Bacillus albus, Bacillus wiedmannii, and a consortium of both species, combined with two compost doses. A completely randomized design with a 3 × 2 factorial arrangement was used, comprising three bacterial treatments and two compost doses (800 and 1200 g), with three replicates per treatment. Total nitrogen, nitrate, nitrite, ammonium, pH, and electrical conductivity were measured at the beginning and after 60 days. Total nitrogen decreased from 1689.24 mg/kg to 485.57–528.61 mg/kg, corresponding to reductions of 68.71–71.26%. The bacterial consortium with 800 g of compost showed the largest numerical reduction (71.26%), although Tukey's test did not detect statistically significant differences among treatment means. In contrast, nitrate increased from 52.63 to 217.50–403.97 mg/kg, with significant effects of bacterial treatment, compost dose, and their interaction (p < 0.0001). Soil pH decreased from 7.21 to 5.70–6.38, while electrical conductivity increased from 85 to 237.67–590.33 µS/cm. The results show changes in soil nitrogen fractions and physicochemical properties across the evaluated combinations. However, the absence of uninoculated control treatments and a nitrogen balance prevents determining the specific contribution of the bacteria to the reduction in total nitrogen.