The agriculture shell wastes were carbothermally converted to magnetic activated carbon by a microwave-assisted decoration of iron oxide nanoparticles onto the shell surface. The influence of ternary catalytic mixtures, including zinc, iron II and III chlorides on the cationic dye adsorption efficiency was addressed by the composite impregnations onto the almond or walnut shell powders, explored to the carbonization. The efficiency was maximized by determination the proportions of used salts. The best results were obtained with loading FeCl3 onto the walnut shell in which the proportion of salt was 50%. Although the load of magnetic particles onto the adsorbent normally lead to decrease in efficiency, the prepared powder exhibited the appropriate performance above 99%. It should be point out that the dye adsorption efficiency of magnetic activated carbons fabricated by carbothermal functionalization was 7–10% higher than those produced in the nitrogen atmosphere. The adsorbent displayed the nano-porous structure with average pore diameter about 2 nm, providing a surface area around 1000 m2·g−1 for the removal of dye in a dynamic system. The maximum adsorption capacity was determined to be 130 mg·g−1 in the neutral condition.