The novelty of the current study deals with the application of a magnetic nanosorbent, chitosan-coated magnetic nanoparticles (cMNPs), to be utilized for the management of lignocellulosic bio-refinery wastewater (LBW) containing three heavy metals and 26 phenolic compounds. The magnetic property of the adsorbent, confirmed by elemental and vibrating sample magnetometer analysis (saturation magnetization of 26.96 emu/g), allows easy separation of the particles in the presence of an external magnetic field. At pH 6.0, with optimized adsorbent dosage of 2.0 g/L and 90 min contact time, maximum removal of phenol (46.2%), copper (42.2%), chromium (18.7%) and arsenic (2.44%) was observed. The extent of removal of phenolic compounds was in the order: polysubstituted > di-susbstituted > mono-substituted > cresol > phenol. Overall, the adsorption capacity (qe) of cMNPs varies among the different contaminants in the following manner: copper (1.03 mg/g), chromium (0.20 mg/g), arsenic (0.04 mg/g) and phenol (0.56 mg/g). Post-adsorption, retrieving the cMNPs using an external magnetic field followed by single-step desorption via acid–base treatment is attractive for implementation in industrial settings. Reusability of the adsorbent was studied by recycling the cMNPs for five consecutive rounds of adsorption followed by desorption, at the end of which, cMNPs retained 20% of their initial adsorption capacity.