Large-scale use of chemical fertilizers has brought about environmental pollution and raised food safety issues besides increasing the cost of production. The present study focused on using natural minerals inoculated with nutrient mobilizing microorganism so-called bio-mineral fertilizer to partially substitute chemical fertilizers dose. Two years of field trials and a pot culture experiment were carried out with pomegranate to look into the possibility of bio-mineral fertilizer use in saving phosphorus (P) and potassium (K) chemical fertilizers application and in improving soil fertility, tree nutrition, and fruit quality. Results manifested that application of biomineral fertilizer significantly enhanced available nitrogen (N), P, and K content of soil and also improved concentration of P, K, magnesium (Mg) and sulphur (S) in the tree foliage. As a consequence, higher fruit yield with perceptible improvement in quality attributes viz. aril percent, 100 arils test weight, juice acidity, ascorbic acid, total phenolics, anthocyanin concentration was observed in bio-mineral treated trees. The highest yield (73.97% increase over control) was recorded with the application of 150 g tree-1 bio-mineral fertilizer which was equivalent to the yield obtained with the recommended dose of P and K chemical fertilizers. In addition, the application of bio-mineral fertilizer led to improvement in the nutritional quality of fruit and also soil microbial environment as indicated by higher microbial biomass carbon and enzymes activities. So, the results indicate that Penicillium pinophilum based bio-mineral fertilizer may be recommended to supplement P and K requirement of pomegranate tree and get maximum benefits in terms of yield, quality, and production cost savings.