The resource-intensive agriculture involving use of chemical fertilizers, irrigation, and tillage practices is a major cause of soil, water, and air pollution. This study was conducted to determine whether integrated use of nutrient, water, and tillage (reduced) can be manipulated to improve the population of plant growth promoting rhizobacteria (Azotobacter, Bacillus, and Pseudomonas) to enhance soil fertility and yield. The study was conducted in the Indo-Gangetic plain (IGP) region of India, where resource-intensive agriculture is practiced. Various combinations of chemical (urea) and organic fertilizers (farmyard manure (FYM), biofertilizer, and green manure) were used on replicated field plots for all the experiments. The effect of integrated resource management (IRM) on activities of Azotobacter, Bacillus, and Pseudomonas and its relation to the yields of rice and wheat crops in subtropical soils of IGP region were also observed. The increased population of all the three microbes, namely, Azotobacter (5.01–7.74 %), Bacillus (3.37–6.79 %), and Pseudomonas (5.21–7.09 %), was observed due to improved structure and increased organic matter in the soil. Similarly, kernel number and 1000 kernel weight were found increased with sole organic N source, three irrigations, and conservation tillage. Thus, it was found that the IRM practices affect the environment positively by increasing the population of beneficial soil microbes and crop yield as compared to high-input agriculture (conventional practices).