The potential interactions of rhizobium bacteria in enhancing nodulation, nitrogen (N) fixation for boosting N availability, and the yield of black gram under a temperate environment continue to remain unexplored. Therefore, this study aimed to evaluate the agronomic performance of black gram cultivars, their yield comparisons, and shoot–grain–soil N dynamics in a prevalently rainfed farming system. Two black gram cultivars, NARC Mash-I and NARC Mash-II, were subjected to rhizobia inoculation combined with different N doses (0, 25, 50, 75, 100 kg ha−1). The response variables included root nodulation, agronomic yield attributes, grain yield, shoot–grain and soil N dynamics, and biological productivity. Black gram cultivar NARC Mash-II showed the maximum nodule formation (41 per plant), while each nodule obtained 0.69 g weight in response to RI combined with 25 kg N ha−1. Additionally, this combination showed the highest pods per plant and thousand grain weight, which maximized the grain yield (1777 kg ha−1) and biological productivity (3007 kg ha−1). In contrast, NARC Mash-I under 50 kg N recorded the highest shoot N content, while the same cultivar under 100 kg N exhibited the maximum soil N content. The correlation analyses indicated a significantly robust association among the nodule numbers, grain weight, and N contents in different plant organs. These results give mechanistic insights into plant–microbe interactions based on the eco-friendly, sustainable, and smart agricultural practice of black gram production in a temperate environment.