This study reports an effective method to explore the significant role of modified chitosan in recovering a protein from starch wastewater of sweet potato. Fourier transform infrared (FT-IR) spectroscopy, energy dispersive X-ray analysis (EDX), polarizing optical microscopy (POM), and scanning electron microscope analysis (SEM) are used to characterize modified chitosan. Parameters, such as agitation time, chitosan dose, initial pH, and settling time, are monitored over the protein recovery process. Also, the second-order polynomial model was developed with Box Behnken design (BBD). 3-D response surface contour graphs are plotted to learn about the interactive effects of process parameters on protein recovery. The optimum operating conditions are determined by using the desired function methodology. Under these optimal conditions, 95% of the protein was recovered. An artificial neural network (ANN)-based model was developed for simulating protein recovery. Electrophoresis analysis has shown that recovered protein can be used as livestock feed ingredients.