Physico-chemical similarities of surface proprieties of calcite and apatite make their separation challenging. Effective flotation separation requires sustainable depressants to mitigate environmental consequences associated with traditional chemical reagents. Here, for the first time we explore the potential of phosphorylated starch (PS) derived from potato waste as a green and effective depressant. Starch was modified using a straightforward phosphorylation process, resulting in PS with a remarkable charge density exceeding 6000 mmol kg−1. The PS was then evaluated for its ability to depress apatite, enhancing the separation efficiency of apatite from calcite in phosphate rock beneficiation via reverse flotation. Micro-flotation experiments revealed PS's distinct depression effect on apatite while minimally impacting calcite. Floatability rates of apatite and calcite were 90.45 % and 92.68 %, respectively. Introducing 10 mg/g PS drastically reduced apatite recovery to <19 %, while calcite recovery remained at 78.80 %. The bench-scale flotation tests demonstrated an upgrading of the phosphate rock to 70,64 % Bone Phosphate of Lime (BPL) with a yield of 89,41 %. Mechanistic studies employing zeta potential (ZP), and wettability analysis elucidated the depression mechanism. Apatite retained hydrophilicity post-PS addition and conditioning with ester, while calcite-acquired hydrophobicity even in the presence of PS. Furthermore, PS exhibited substantial adsorption onto the apatite surface through chemical reactions involving the phosphate groups and the activated calcium sites on the apatite. Overall, PS stands out as a promising, eco-friendly, and remarkably efficient depressant for separating apatite from calcite through flotation.