Chemical (synthetic) fertilizers used indiscriminately for improved production pose a major threat to long-term soil fertility, the soil environment, and its components. The soil microbial community, however, plays a major and important role in fostering soil health and plant growth. While the use of synthetic fertilizers has a profound impact on plant growth, it also significantly alters the makeup of the microbial community towards a detrimental low, especially N and P fertilizers. Sustainable farming practices can reduce the depletion of natural resources and maintain both productivity and soil fertility. The use of minerals that contain fertilizer nutrients in their native state is a very promising approach to reducing emissions associated with the processing chemical industries. Organic material from natural sources (food waste, manure from livestock, agricultural biomass, etc.) acts as a source of microbial culture and encourages the release of nutrients into the soil during mineral weathering. The combination of nutrient-bearing minerals and their biological weathering agents together with organic matter has the potential to remediate, restore, and sustain depleted agricultural soils. Therefore, in this review, we emphasize the significance of sustaining agricultural productivity and microbial diversity in the rhizosphere, the two vital aspects of modern agricultural systems, through bio-organic mineral fertilizers.