Herein, a novel magnetic nanocomposite (Fe3O4@ATPA@AMPA) was successfully synthesized for the removal of malachite green (MG) from water. The FT-IR analysis confirmed successful modification of Fe3O4@ATPA with 2-Amino-3-mercaptopropionic acid (APMA). Based on TEM image and XRD pattern, the average particle size of Fe3O4@ATPA@AMPA nanocomposite was ∼ 12.3 nm. The specific surface area of Fe3O4@ATPA@AMPA nanocomposite was 35 m2/g. Elemental analysis exhibited the existence of S, O, C, and N on the surface of Fe3O4 nanoparticles. The influence of time (t: 5–240 min), dose (m: 0.010–0.050 g), pH (2–8.5), initial MG concentration (Co: 25–300 mg/L), and temperature (T: 298–318 K) on the MG adsorption was examined. Experimental results exhibit optimal MG uptake at pH: 6.7, t: 120 min, m: 20 mg, T: 298 K, and Co: 300 mg/L. The non-linear kinetics and isotherm models showed that the adsorption process obeyed pseudo-first-order kinetic and Langmuir isotherm models, respectively. According to Dubinin–Radushkevich (D–R) isotherm, the magnitude of activation energy (Ea) at varied temperatures was in range 0.0116−0.0905 kJ/mol, confirming physical interactions between MG molecules and Fe3O4@ATPA@AMPA nanocomposite dominates during adsorption. The maximum monolayer adsorption capacity for MG was 414.63 mg/g at 298 K. The adsorption process was exothermic, favorable, and spontaneous. Finally, the Fe3O4@ATPA@AMPA nanocomposite exhibited excellent adsorption potential for four consecutive regeneration cycles.