In our study, a phosphorus-based mineral fertilizer was obtained through the neutralization of acidic wastewater from cotton soapstock production using a mineral mass rich in carbonate from the Central Kyzylkum phosphorite deposit. The acidic wastewater was employed as a medium for the activation of partially inert phosphorite. The activation reaction was conducted at various mass compositions (from 100:10 to 100:40) and under controlled conditions (333 K, 300 rpm, and a reaction time of 30 minutes). The products’ chemical composition was investigated in terms of total P2O5 content and bioavailable phosphorus in citric acid-soluble and Trilon B-soluble fractions. Optimal ratio conditions were achieved at a composition of 100:20, under which a desirable pH level and the highest bioavailable phosphorus content were achieved. The effect of our phosphorus fertilizer produced under optimal ratio conditions on agricultural growth was also demonstrated in tests involving cotton seeds. The tests clearly showed a significant increase in germination speed, length, and weight of the produced seeds in comparison to the control variant. The findings were further confirmed through statistical analysis (p < 0.05). This method is an exemplary and ecologically benign means of reutilization for industrial-scale acidic wastewater and phosphorite production waste in the synthesis of a highly valuable and useful phosphorus-based mineral fertilizer.