Black sesame pigment (BSP) was shown to bind lead, cadmium, and mercury at pH 7.0 and to a lower extent at pH 2.0. BSP at 0.05 mg/mL removed the metals at 15 μM to a significant extent (>65% for cadmium and >90% for mercury and lead), with no changes following simulated digestion. The maximum binding capacities at pH 7.0 were 626.0 mg/g (lead), 42.2 mg/g (cadmium), and 69.3 mg/g (mercury). In the presence of essential metals, such as iron, calcium, and zinc, BSP retained high selectivity toward heavy metals. Model pigments from caffeic acid, ferulic acid, and coniferyl alcohol showed lower or comparable binding ability, suggesting that the marked properties of BSP may result from cooperativity of different sites likely carboxy groups and o-diphenol and guaiacyl functionalities. Direct evidence for the presence of such units was obtained by structural analysis of BSP by solid-state Fourier transform infrared spectroscopy and 13C nuclear magnetic resonance spectroscopy.