While extensive research has been performed on the composition and cooking quality of commodity beans, relatively little is known about pigmented heirloom varieties and the effects of processing on their antioxidant capacity. The aim of this study was to evaluate the effect of soaking and cooking on antioxidants in four heirloom bean varieties compared to Pinto. Water absorption kinetics, soaking and cooking time, DPPH radical scavenging activity, and total phenolic and total flavonoid content were determined in raw, soaked, and cooked samples. Heirlooms required less time to hydrate compared to Pinto, whereas cooking times were similar. The effect of soaking on antioxidant capacity and flavonoids was minimal compared to cooking, which led to losses of up to 57%. Each pigmented heirloom bean had specific characteristics, and three of them had equal or higher amounts of antioxidants or antioxidant activity than Pinto at every processing step. Among heirlooms, Koronis Purple and Jacob's Cattle had the highest antioxidant activity and Jacob's Cattle and Tiger's Eye the highest amount of flavonoids, even after cooking.