Carob fruit utilization remains limited, with most of their commercial value derived from locust bean gum, which is obtained from seed endosperm. Efficient extraction requires dehusking, which is traditionally performed under harsh conditions. This study aims to develop and optimize a milder, more sustainable dehusking method while preserving seed quality for industrial applications. Various aqueous-based solvents were tested, leading to the selection of metanesulfonic acid (CH4O3S). A Box–Behnken design with response surface methodology optimized the process, using husk removal efficiency as the response variable. The optimized conditions were 24.5 g of seeds treated in 50 mL of a solvent mixture (41% CH4O3S and 59% H2SO4) at 90 °C for 10 min, followed by washing by 5 min with water (87 mL). The treated seeds were analyzed using colorimetry assays and diffusive reflectance spectroscopy and benchmarked against both pristine and dehusked seeds from a local company. The resulting seeds remained morphologically intact and exhibited appealing color characteristics comparable to commercial samples. The optimized method ensured intact seed morphology and color characteristics comparable to commercial standards, offering a viable alternative to conventional H2SO4-based dehusking. Furthermore, this study also highlights for the first time the effectiveness of diffusive reflectance spectroscopy as a rapid and straightforward tool for assessing the dehusking process.