The present study has been designed to utilize industrial and agricultural solid waste for NPK (Nitrogen–Phosphorus–Potassium) bio-organic fertilizer production and its optimized use. The collagenic material of wet blue leather (WBL) from leather industry was used as nitrogen source, after H3PO4 acid-mediated chromium removal. Chicken meat-bone meal (CMBM) and rice husk ash (RHA) are abundantly available locally, had used as P, K, and Ca sources. The presence of N, P, K, Ca in the produced bio-organic NPK fertilizer were 10.76, 11.03, 3.41, 13.64, respectively as per mixing ratio of ingredients. In this study it was effect on the chili plant (Capsicum annuum L.) growth and revealed 1.15 and 1.03 fold higher plant growth, 1.40 and 1.18 fold higher total chlorophyll content than untreated soil (control), and chemical fertilizer. The liberation of fertilizers components from their source, transport of fertilizer components in the soil, and absorption in plant roots have been studied using mathematical models indicating the optimum fertilizer use for better productivity and to reduce loss of extra fertilizer and eutrophication. The formulation showed excellent water retention capability (3.2 L/kg), which might increase soil water availability to the plants and eventually reduce water demand and labour cost. DNA intercalation study proved there is no harm to use this fertilizer.