This study intended to determine the ability of endophytic bacteria recovered from root nodules of Cicer arietinum L. and Vigna unguiculata L. (Walp.) plants to synthesize exopolysaccharide (EPS) and to enhance the production by changing nutritional factors. Twenty endophytic bacteria isolated from root nodules of Cicer arietinum and Vigna unguiculata were tested for their production of EPS. High EPS-producing isolates were identified on phenotypic and genotypic characteristics. Among 20 isolates, Stenotrophomonas maltophilia (C6) and Brevibacillus parabrevis (V4) isolated from root nodules of Cicer arietinum and Vigna unguiculata produced a high EPS yield in comparison with other isolates. Using 1% of sucrose as sole carbon source increases the concentration of EPS produced by S. maltophilia and B. parabrevis (65 and 107%, respectively). EPS produced by S. maltophilia and B. parabrevis was increased by the addition of fructose and lactose (0.1%). Addition of 1.68 g/L KNO3 or 2.49 g/L glycine to modified yeast extract mannitol medium (YEMB) significantly increased EPS production by S. maltophilia and B. parabrevis. Furthermore, the presence of Fe3O4 nanoparticles (25–50 µg/mL) in the modified YEMB medium increased EPS yield by B. parabrevis. Chemical characterization of EPS by GC–MS and FTIR indicate that the EPS biochemical composition is dependent on the bioavailability of carbon substrates and is controlled by limiting nutrients. The combination of the best two carbon sources sucrose (0.9%) and fructose or lactose (0.1%) in the presence of KNO3 or glycine as the best nitrogen sources significantly increased EPS yield of S. maltophilia and B. parabrevis, respectively.