Plant residues, comprising organic materials derived from agricultural, food, and other plant-related activities, represent a significant resource with immense potential for sustainable utilization. This entails converting plant residues into products of economic, environmental, or social value, thereby contributing to circular economy principles and sustainable development goals. Water pollution, a pressing global issue, necessitates effective and sustainable treatment methods. Traditional chemical coagulants, while effective, often pose environmental concerns due to their synthetic nature and potential toxicity. This research explores the potential of natural bio coagulants, which is a residue generated during the extraction of oil from onion seeds (REO), as a greener alternative for removal methyl green in aqueous solutions. The FTIR of REO after bio coagulation shows distinct peaks corresponding to various functional groups, such as O–H, C−H, C=O, C=C, and C−O, indicating the complex composition and the changes due to loading with MG. The method of Boehm showed that bio coagulant a slightly acidic character. The pH of the zero charge point was pHPZC = 6.2, confirming its low acid character. The optimization of applicability of natural bio coagulants is necessary for sustainable water management. In this study the REO was tested as biocoagulant for reduction of methyl green (MG) in aqueous solutions. It has demonstrated significant effectiveness in the coagulation process, where the concentration of MG was reduced from 10 mg/L to 2.74 mg/L, achieving a yield of 72% without adding floculants and when C0 = 10 mg/l, pH = 5.9, and T = 22 °C.