After being subjected to different cooking methods, small black beans (Rhynchosia nulubilis) were investigated in order to assess the effects of the retained bioactive compounds. Using uncooked, pan broiled, boiled, steamed, and pressure cooked beans, the inhibitory effects of MCF-7 cell migration were evaluated at protein concentrations of 40, 160, and 640 μm/mL, using the Boyden's chamber assay. All protein concentrations (40, 160, and 640 μm/mL) of pan broiled beans showed significant reduction (59.83, 32.48, and 21.37%, respectively) in the rate of cell migration to the lower chambers (p-value less than 0.001). Estimated cell migration rates correlated to the exponential decay between experimentally measured cell migration rates and converted samples. The range of estimated cell migration rate for each 100 mg/mL of cooked sample was as follows: pan broiled (21.16%), boiled (22.48%), steamed (22.48%), pressure cooked (29.52%), and uncooked (35.03%) beans. Our study indicated that selective modifications of cooking methods for small black beans, such as pan broiling, ameliorated the inhibitory effects of MCF-7 cell migration. This suggests that optimized cooking methods increase the nutritional contents of the cooked food.