Glyphosate as an effective broad-spectrum herbicide is frequently detected in various water and soil resources. Given the ubiquity of β-MnO2 and δ-MnO2 colloids in groundwater and soil, the abiotic removal of glyphosate by MnO2 colloids was investigated. β-MnO2 colloids exhibited superior glyphosate removal efficiency, up to 37%, compared to 21% for δ-MnO2 colloids at a pH of 4.0. Glyphosate removal involved simultaneous adsorption and oxidation process, identified by HRTEM, NH3-TPD, XPS, LC-MS, FTIR analyses and the occurrence of aminomethylphosphonic acid (AMPA) and Mn2+. Moreover, adsorption dominated the removal of glyphosate by two MnO2 colloids. The solution pH had a substantial effect on glyphosate removal. Co-existing ions in the solution, such as carbonate (CO32−), phosphate (Na2HPO4, NaH2PO4) and humic acid (HA), were also found to impede glyphosate removal. Phosphate, in particular, exhibited a strong competitive effect for adsorption sites on both MnO2 colloids. Of them, the removal of glyphosate by β-MnO2 colloids was more prone to occur due to its higher specific surface area, abundant oxygen vacancies, and moderate acid sites. However, δ-MnO2 colloids presented a stronger oxidation capacity than that of β-MnO2 colloids due to the quicker generation rate of Mn2+. Finally, AMPA was the same products by two MnO2 colloids in the oxidation process, revealing the degradation pathway based on the cleavage of C–N bond. Therefore, by comparing kinetics and mechanisms of glyphosate removal by β- and δ-MnO2 colloids, this study improves us better understanding for the behavior of glyphosate in the environment.