This study aimed to evaluate the impact of thermal processing and soaking on the profiles and contents of phenolic compounds in brown beans, as well as their antioxidant activity. We evaluated the antioxidant activity of extracts and the contents of phenolic acids and flavonoids by high-performance liquid chromatography (HPLC). With the exception of chlorogenic acid, the contents of all of the other phenolic acids were increased by cooking. Kaempferol was only detected in samples treated by soaking followed by cooking. Catechin and kaempferol-3-glucoside were found in all of the brown bean extracts. Cooking, with or without soaking, caused significant increases in the concentrations of quercetin and quercetin-3-glucoside only. The effect of the heat treatment increased the antioxidant activity and the concentrations of the phenolic compounds evaluated.