Nodule associated endophytic yeasts have attracted much attention due to its potential plant growth-promoting activities and protecting legume crops from both biotic and abiotic stress. The present study evaluated the potential role of an endophytic yeast Candida tropicalis VYW1 in modulating host fitness (blackgram) both as a single inoculant and co-inoculant with Rhizobium sp. VRE1. The results showed that nodule associated endophytic yeast C. tropicalis VYW1 when co-inoculated with Rhizobium sp. VRE1 significantly increased the germination percent (100%), root (34.6 cm), and shoot length (32.8 cm). The vigor index was also maximum (4250) in the treatment that received the co-inoculation of Rhizobium sp. VRE1 and C. tropicalis VYW1 besides registering enhanced hydrolytic enzyme, α-amylase, and protein content in seeds. Metabolite profiling of bacterial primed seed exudates revealed 30 diverse compounds belonging to the classes viz., sugars, amino acids, organic acids, flavones, prenol lipids, and fatty acids. The blackgram seeds primed with co-inoculants released hydroxyl benzoic acid and galactopyranose, which act as potential chemoattractants and involves in the lectin complement pathway regulating fructose mannose metabolism. These metabolites lead to a significant increase in germination and nodulation in blackgram seedlings. Hence, the study suggests the scope of enhancing the fitness of blackgram using a co-inoculant comprising of C. tropicalis VYW1 and Rhizobium sp. VRE1.