The subject of the invention is a method for modification of natural coffee beans in order to remove irritating substances without the loss of its useful features, such as caffeine contents, sensory and anti-oxidation properties.A method for modification of natural coffee beans, consisting of removing irritant substances, characterized in that green coffee beans or mixture of green coffee beans are immersed in a water solution of natural di- and tri-carboxyl organic acids with a concentration in the range of 0.5 to 10 g/l, advantageously 5 g/l, after which it is extracted for 0.5-10 hours, advantageously 5 hours, then the solution in which the beans were immersed is decanted, the beans are flushed with water, and then dried with hot air at a temperature of 40-150°C until the beans reach a humidity below 15%, then the beans are subjected to a roasting process in a known method.