ynthetic toxic dyes from liquid wastes can be harmful for living organisms and the environment, even at low concentrations. This research investigated the utilization of the Chenopodium quinoa pericarp bio-waste (QBW) after saponin glycosides extraction as biosorbent in the removal of methylene blue (MB) dye as a model contaminant from aqueous solution. QBW was successfully modified by chemical (sulfuric acid) and thermal (pyrolysis) treatments. The biosorbent was characterized by FTIR, TGA, BET, Zeta Potential, SEM/EDX, and contact angle analysis to get further insight into the adsorbent’s behavior and to propose a suitable biosorption mechanism. Batch experiments were explored to study the effect of various parameters on MB removal efficiency, including contact time, adsorbent quantity, initial concentration, and process temperature. The optimum conditions for QBW biosorption of MB were at neutral pH and contact time of 60 min. The maximum adsorption capacity of the biosorbent (QBW-II), which demonstrated the highest MB removal efficiency in the biosorption test was 193.802 ± 4.365 mg.g−1. The kinetic and isotherm study of MB dye biosorption revealed that the pseudo-second-order model and Langmuir isotherm were the best fit. Thermodynamic parameters for the biosorption showed that the process was spontaneous and exothermic. Our findings demonstrate that QBW has a high potential to be used as an environmentally friendly and promising bio-sorbent to effectively remove organic contaminants from aqueous systems.