The mono and binary biosorption of Cu(II) ions, Ni(II) ions, and Methylene Blue dye onto raw and pretreated S. cerevisiae was investigated in a batch system. The biosorption mechanism was characterized by FT-IR, XRD, and SEM analyses. The effects of pH, contact time, initial pollutant concentration, temperature, and biosorbent dosage on the biosorption studies were determined. The experimental data were analyzed by Langmuir, Freundlich, and Dubinin-Radushkevich isotherm models. The results were compatible with both Langmuir and Freundlich isotherm models. The mean free energy (E) values indicated that the biosorption of Cu(II), Ni(II), and Methylene Blue onto raw and pretreated S. cerevisiae took place by chemical-ion exchange. Kinetic data fitted well into the pseudo-second-order model. The calculated thermodynamic parameters (Delta H, Delta S, and Delta G) showed that the biosorption of Cu(II), Ni(II), and Methylene Blue onto raw and pretreated S. cerevisiae was exothermic and spontaneous. Desorption, ion selectivity, and the effect of ionic strength (NaCl) studies were also conducted. Competitive biosorption of binary mixtures of Cu(II), Ni(II), and MB was investigated in terms of biosorption capacity and found that the biosorption capacity of biosorbent decreased with increasing competing pollutant concentration.