This study aims to assess the ability of old, immobilized fresh, and free fresh green microalgae (a Bracteacoccus sp.) to remove methyl orange (MO) dye from aqueous solutions. The effects of four factors, including initial MO concentration (5–25 mg L−1), adsorbent dose (0.02–0.10 g mL−1), temperature (4–36 °C), and contact time (5–95 min), were examined. The Box–Behnken design (BBD) was used to determine the number of required experiments and the optimal conditions expected to provide the highest removal percentage of MO dye from aqueous solutions. The experimental data were applied to four isotherm models (Langmuir, Freundlich, Dubinin–Radushkevich (D–R), and Temkin isotherm models) and three kinetic models (pseudo–first–order, pseudo–second–order, and Elovich kinetic models). The results indicate that the highest removal of MO (97%) could be obtained in optimal conditions consisting of an initial MO concentration of 10.0 mg L−1, an adsorbent dose of 0.10 g mL−1, a temperature of 20 °C, and a contact time of 75 min. Moreover, the experimental data were best fitted by the Langmuir and Temkin isotherm models and followed a pseudo-second-order kinetic model. The interaction between MO and the Bracteacoccus sp. was confirmed by UV and ESI/MS analyses, indicating that MO removal occurred via both sorption and degradation processes.