This study aimed to utilize cationic protein extracted from the Moringa oleifera seed in the fabrication of cationic starch crosslinked with magnetic nanoparticles (MagCS). Important synthesis parameters include starch to cationic protein volume ratio, magnetic nanoparticles mass fraction, reaction and crosslinking time, reaction and crosslinking temperature and crosslinker concentration. At optimum synthesis conditions, MagCS yield a 38.55% amide content, 2.46 degree of substitution, 1.1 mmol/g charge density and 78.6% crosslinking, which are much higher compared to other starch derivatives. A series of characterization analyses such as Fourier transform infrared spectroscopy, X-ray diffraction, thermogravimetric analysis, elemental analysis and vibrating sample magnetometer concluded that MagCS was embedded with amide group, has high crystallinity structure, is thermally stable and shows a promising magnetic characteristic. Based on the synthesis parameters and characterization studies, the synthesis mechanism of MagCS was also postulated. The flocculation performance of MagCS was successfully assessed for the treatment of palm oil mill effluent. At optimum dosage, initial pH and settling time of 1.0 g/L, 9.0 and 15 min, the MagCS flocculant was able to remove 90.48, 83.95 and 58.19% of turbidity, color and chemical oxygen demand, respectively. This study provides an alternative eco-friendly materials in the wastewater treatment application.