Cassia fistula seed-derived coagulant has been reported to exhibit high coagulating–flocculating activity, environmental friendliness, and cost-effectiveness for the wastewater treatment, especially of textile wastewater. For heavy metal removal, however, research focusing on evaluating the feasibility of this material is still limited. Therefore, this study reports jar-test experiments in which the Zn2+ and Ni2+ removal efficiency of C. fistula coagulant was assessed. Moreover, a comparison of coagulation performance using a conventional chemical coagulant and the natural coagulant was performed. Characterization of the C. fistula seed-derived coagulant revealed the presence of important functional groups and fibrous networks with rough surfaces. A bench-scale study indicated that the coagulation performance of the two coagulants depends strongly on the initial concentration of metal ions, pH level, and coagulant dosage. The C. fistula seed-derived coagulant was found to possess higher removal efficiency than polyaluminum chloride. This natural coagulant removed over 80% of metal ions at the optimal conditions of pH 5.0, a metal ion concentration of 25 ppm, and a dosage of 0.8 and 1.6 g/L for Zn2+ and Ni2+, respectively. This study shows that C. fistula seed-derived coagulant is a potential alternative to chemical coagulants and could be developed to provide an environmentally friendly, economical, and efficient wastewater treatment.