Flotation separation of Cu–Fe sulfide minerals typically necessitate the addition of substantial quantities of lime to depress pyrite flotation. Because lime can harm the environment, there is an urgent need to develop novel environmentally friendly depressants that are non-toxic and biodegradable. In this study, we investigated an environmentally friendly pyrite depressant containing amino and carboxyl groups, namely D-arginine (DA). The effect of DA on the surface hydrophobicity of Cu–Fe sulfide minerals and thus collector adsorption was investigated by analyzing zeta potentials, adsorption capacities, and contact angles. Additionally, changes in the surface properties of the minerals induced by DA were examined using X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectroscopy (ToF-SIMS), and atomic force microscopy (AFM). Flotation tests revealed that 2 × 10–4 mol/L DA reduced the flotation recovery of pyrite to 9.96 % at low alkalinity while leaving chalcopyrite recovery unchanged. The results of mineral surface analysis indicated that DA exhibited significantly stronger adsorption on the pyrite surface than on the chalcopyrite surface. Furthermore, DA effectively reduced the adsorption of the collector on the surface of pyrite, thereby weakening pyrite floatability at low alkalinity. Therefore, DA is a promising alternative depressant for the flotation separation of chalcopyrite from pyrite.