The examination of the performance of raw and immobilized S. (Saccharomyces) cerevisiae in the simultaneous abatement of metal ions from wastewater effluent is the focal point of this article. The optimal storage time for raw and immobilized S. cerevisiae, during which they can be utilized, was estimated. The outcomes revealed that as the initial metal ion concentrations increased, the adsorption capacity improved, while the removal efficiency of S. cerevisiae yeast cells decreased, with the highest uptake obtained at the optimal conditions: pH = 5.0, 2.0 g S. cerevisiae/L, 25 °C, and a contact time of 25 min. The maximum adsorption capacities (qmax) for Pb(II), Cd(II), and Ni(II) ions are shown by Langmuir at 65, 90, and 51 mg/g, respectively. It was discovered that the metal ions’ biosorption reactions were spontaneous and were fitted by the pseudo-second-order model. The mechanisms of the metal ions’ abatement were explained by using XRD (X-ray diffraction), FTIR (Fourier transform infrared spectroscopy), (BET) Brunauer–Emmett–Teller, and TEM (transmission electron microscopy) outputs. EDTA and citric acid can eliminate more than 70 ± 4 and 90 ± 5% of the adsorbed ions, respectively. The experiment of storage demonstrated that the immobilized S. cerevisiae was more stable for 8 months than the raw yeast.