This study investigated the comparative effects of mixed nanocomposite (MNC) fertilizers as an alternative to commercial fertilizers (CFs) on endophytic symbiosis and nutritional properties of rice grains. We synthesized MNC fertilizers with different concentrations and characterized them by using scanning electron microscopy and Fourier transform infrared spectroscopy. The CF was applied as per the method followed by local farmers; however, for MNC fertilizers both foliar and soil applications were done. Comparative analysis of growth and development, rice-endophyte symbiosis, and nutritional properties of rice grains was conducted. The panicles per hill, length of panicles, grain per panicles, 1000-grain weight, and dry matter of rice plants treated with MNC fertilizers were found to be not statistically ( p  > 0.05) different compared to those of CF. However, growth parameters were significantly ( p  < 0.05) higher in MNC fertilizer-treated crops than in CF-treated crops. Several predominant endophytes such as  Penicillium  spp.,  Aspergillus fumigatus ,  Rhizopus  spp., and  Fusarium  spp. that could have significant effects on the enhancement of growth and nutritional properties of rice grains were identified in rice plants treated with MNC fertilizers at different concentrations. Contrarily, stem-associated  Cercospora  spp. was found in the CF-treated field and fission yeast was observed in the blank-treated field. In addition, the contents of proteins, fibers, carbohydrates, energy-yielding components, vitamin A, and minerals were significantly increased in rice plants treated with MNC fertilizers. Thus, we would like to conclude that MNC fertilizers could be one of the most potential alternatives to CFs for achieving better rice-endophyte symbiosis as well as nutritional improvements in rice grains for sustainable production.