The use of natural phosphate rock as a source of phosphorus for plant growth is considered more environmentally friendly, compared to conventional chemical fertilizers. However, the very low solubility of the phosphate present in natural rocks limits its practical application. To overcome this limitation, a composite was developed based on the dispersion of nanoparticulate phosphate rock in a polysaccharide matrix of starch, as an integrated strategy to facilitate application and provide a supporting substrate for an acidulant microorganism, Aspergillus niger. The bioactivation of the nanocomposite resulted in a remarkable solubilization of up to 70% of the total available phosphate in very low solubility phosphate rocks (Bayovar and Itafos) and 100% of the total available phosphate in a reference mineral (hydroxyapatite), in only 96 h. Such approach employing bioactivation of starch-phosphate rock nanocomposites significantly contributed to improve P-solubilization, opening new routes for the development of smart fertilizers based on polysaccharide matrix.