Fertilization management of pigeon peas can increase soil quality and the N utilization by plants. Therefore, we evaluated the biological activity of soil cultivated with pigeon peas (Cajanus cajan (L) Millsp.) under different fertilization treatments. A randomized block design was used with three replicates and a 3×5 factorial arrangement (genotype×fertilization and inoculation management). At full flowering stage, the plants were collected and shoot dry matter was evaluated. Soil was sampled at 0-20 cm for various analysis viz. nodulation assessment; soil organic carbon; total nitrogen; carbon and nitrogen from microbial biomass; C/N ratio; β-glucosidase and urease enzymatic activity. Data were subjected to analysis of variance and Tukey’s test (P ≤ 0.05). A Pearson correlation matrix was constructed, and the similarity between treatments was evaluated using the Mahalanobis distance and grouping was done using the unweighted pair group method with arithmetic average (UPGMA). Both the experimental genotypes (BRS03 and BRS04) showed similar nodulation and shoot dry matter pattern with respect to fertilizer treatments. Furthermore, the microbial inoculation promoted a higher shoot dry matter content in all the genotypes. The application of mineral N and inoculation increased the total N content in the soil, favoring the mineralization of this nutrient. During the testing phase, the genotypes exhibited an increase in microbial carbon and microbial quotient levels, indicating an improvement in soil quality. The combination of fertilization and inoculation increased the enzymatic activity of β-glucosidase and urease. The correlation matrix showed a strong association between N total and C/N ratio. The formation of groups by UPGMA was observed as a function of inoculation, demonstrating its effect on soil biological variables.