Chemical fertilizers are overused, so people across the world are now looking for environmentally friendly ways to cultivate crops. The impact of biofertilizer use on soil, crop production and microbiological activity is studied in wheat and maize. The work was completed in different parts of Pakistan, where four combination approaches were assessed: a control, NPK fertilizer, biofertilizer-only and an approach of 50% NPK joined with biofertilizer. Biofertilizer and combined treatments increased soil organic carbon, nutrients, bacterial and fungal population and activity levels of enzymes more than the control and NPK-only plots. Moreover, important benefits could be seen in plant development, as the root length, shoot height, chlorophyll levels, and total grain yield all improved. The inclusion of treatment in the experiment slightly improved maize and wheat yields by up to 100% and 82.1%, respectively. The use of biofertilizers led to a significant rise in the population of helpful genera such as Bacillus, Pseudomonas, and Rhizobium, which improved nutrient use and the plant’s tolerance to stress. Evidence of many microorganisms being linked to high crop numbers supports the idea of the importance of biology in soil for sustainable farming. According to these results, using efficient biofertilizers can help boost crop output, protect the soil, and support the overall balance of the environment, providing an eco-friendly alternative in farming.