The objective of this study was to investigate the possibility of using natural and bacteria-modified Erzurum clayey soil with Methylobacterium extorquens as an alternative to high cost commercial adsorbent materials for the removal of copper from aqueous solution. The copper concentrations in the samples of the polluted river water and CuCl2 solutions treated by the natural and bacteria-modified Erzurum clayey soil (ECS) have been determined by spectrophotometric method. Firstly, the surface of ECS was modified with M. extorquens and surface functionality was increased. Then, the adsorption of Cu (II) from solution phases was studied with respect to varying metal concentration, pH, and temperature and agitation time. The maximum adsorption of Cu (II) for natural and bacteria-modified Erzurum clayey soil was observed at pH: 5.0. At different copper concentrations, copper adsorption analysis was performed on 1 g using clay soil or modified clay soil. Maximum adsorption of Cu (II) was obtained as 45.7 and 48.1 mg g-1 at initial concentration (50 mg/50 mL) and optimal conditions by natural and bacteria-modified clay soil, respectively. The copper concentration was decreased in the substantial amount of the leachates solutions of natural and bacteria-modified clay soil. Langmuir and Freundlich isotherms were used to describe the adsorption behavior of Cu (II) ions. The results showed that modified clay soil had a high level of adsorption capacity for copper ion. The various thermodynamic parameters such as ΔG°, ΔH° and ΔS° were analyzed to observe the nature of adsorption. The structural properties of the natural and bacteria-modified-ECS have been characterized by SEM, FTIR and XRD techniques. Consequently, it was concluded that the bacteria-modified clay soil could be successfully used for the removal of the copper ions from the aqueous solutions.