Nitrogen (N) availability and soil microbiota exert significant impacts on plant metabolic systems and yield. Different studies have indicated that yield and nitrogen use efficiency (NUE) of pearl millet (Pennisetum glaucum L.R.Br.) can be improved by the inoculation of N-fixing bacteria. However, the interactive effects of different N sources and bacteria inoculation on growth, productivity, and NUE of pearl millet have been less explored. Therefore, individual and interactive effects of different N sources (organic and inorganic) and bacteria inoculation on growth, productivity, and NUE of pearl millet were investigated in this study. Two different N sources, i.e., organic (farmyard manure) and inorganic (urea) alone or in 50% + 50% combinations (urea + FYM), were used to supply the recommended amount of N. Similarly, seeds were inoculated with two different N-fixing bacteria, i.e., endobacteria (Enterobacter sp. MN17) and rhizobacteria (Stenotrophomonas maltophilia FA-9). Urea + farmyard manure (FYM) and seed inoculation rhizobacteria improved soil attributes, yield-related traits, grain quality, NUE, and net economic returns. Soil porosity was significantly improved by seed inoculation with both bacteria and FYM application. Similarly, seed inoculation with rhizobacteria increased soil organic carbon by 45.45% and 34.88% during the 1st and 2nd year of the study, respectively. Urea + FYM application combined with rhizobacteria seed inoculation improved the number of grains per ear (23.49 and 23.63%), 1000-grain weight (5.76% and 7.85%), grain yield (23.19% and 25.0%), and NUE (33.83 and 48.15%). Similarly, grain quality was significantly improved by seed inoculation with both bacteria. Likewise, urea + FYM combined with rhizobacteria improved nitrogen use efficiency (NUE) by 33.83% and 48.15% in 2020 and 2021, respectively, compared to no N application and no seed inoculation. The highest economic returns (1506.4 and 1506.9 USD) were noted for urea + FYM application combined with rhizobacteria seed inoculation. Therefore, urea + FYM application combined with rhizobacteria (S. maltophilia FA-9) seed inoculation seemed a viable approach to improve grain yield, grain quality, NUE, and net economic returns of pearl millet.