The field experiment was conducted during the kharif and rabi seasons of 2022–23 and 2023–24 at the Agronomy Main Research Farm, College of Agriculture, Odisha University of Agriculture and Technology, Bhubaneswar, Odisha, to identify the performance of pigeon pea in rice-based cropping systems and its implications on soil biochemical indicators. The experiment was laid out in a randomised block design (RBD) with 12 treatments and 3 replications. Recommended dose of fertilisers for rice was 80:40:40 kg N, P2O5, K2O ha-1. N was applied as per treatment; NU spray dose was 2 sprays at 30 and 50 DAT and basal application of P and K at 40 kg each ha-1 and ZnSO4 at 25 kg ha-1. The pigeon pea variety “PRG-176” was grown under residual nutrient conditions in the rabi season. The soil of the experimental site was sandy loam in texture, acidic in reaction (pH 5.04), medium in available organic carbon (5.23 g kg-1), EC (0.02 dSm-1), low in available nitrogen (213.3 kg ha-1), medium in available phosphorus (16.3 kg ha-1), medium in available potassium (134.4 kg ha-1), low in available sulphur (12.9 kg ha-1) and zinc (0.52 kg ha-1). In pigeon pea grown under residual condition in rabi season, the maximum plant height (145.7 cm), primary branches (14.4 plant-1), secondary branches (19.9 plant-1), dry matter accumulation (99.96 g plant-1) at harvest, number of pods (131.8 plant-1), number of seeds per pod (4.4), seed index (11.5 g), seed yield (1394.1 kg ha-1) and haulm yield (5060.1 kg ha-1) was recorded when 75 % STBN + 25 % VC + ZnSO4 (T9) was applied to rice and it was at par with 75 % STBN + 25 % FYM + ZnSO4 (T8), 75 % STBN + 25 % VC (T3) and 75 % STBN + 25 % FYM (T2). After two years of experimentation, the organic carbon content, microbial population (bacteria, fungi and actinomycetes), microbial biomass carbon (MBC), microbial biomass nitrogen (MBN) and activity of soil enzymes like urease, dehydrogenase, acid and alkaline phosphatase improved over the initial value in the rice-pigeon pea system.