The primary objective of this study is to find the potential of biochar made from five different types of agricultural waste (straw, cow dung, sludge, food waste, and lawn grass) as a cost-effective adsorbent to remove coloring pigments from aqueous solutions. The biosorption of Malachite Green, a cationic dye, onto modified agro-waste-derived biochar demonstrated that specific modifications enhanced the adsorption capacity of the adsorbent. Adopting a combination of carbonization, microwave irradiation, and sonication to modify the biochar with activation was the most effective way to completely remove malachite green from the aqueous phase. The batch adsorption studies were conducted by varying various operational parameters such as pH, initial concentration of adsorbate, adsorbent dosages, contact time, and the aqueous phase temperature which were optimized to evaluate the adsorption behavior of the biomass. The experiments were performed by varying the pH in the range 2–10, contact time was varied in the range 0–140 min, adsorbent dosage was varied in the range 0–15 mg, adsorbate concentration varied in the range 0–100 mg per L, and temperature was varied in the range 25–35 °C. The optimum conditions were as follows: the equilibrium time was 90 min, optimum pH was 7.0, optimum concentration of adsorbate was 50 mg per L, and adsorbent dosage was 7.5 mg/g. The maximum adsorption removal efficiency at the optimum conditions was observed to be more than 85% for activated biochar and 60% for non-activated biochar. The maximum adsorption capacity was obtained to be 0.355 mg per g for malachite green dye by using Langmuir isotherm model. The thermodynamic parameters with ΔH° and ΔS° values are 8024.32 J per mol and 32.8 J per mol per K respectively, which show that adsorption processes are endothermic in nature, entropy-driven, and non-spontaneous. The results shows that the low-cost biomass possesses the potential for the effective removal of dyes from wastewater.