The invention provides a method of processing green coffee beans that improves the aromas and flavors of green coffee beans through simple means, allowing richly fragrant green coffee beans that have unique aromas to be obtained with ease. A method of processing green coffee beans includes a fermentation process by bringing green coffee beans, which are unground seeds from coffee berries, microorganisms, and nutritive substances that are metabolized by the microorganisms into contact with one another to cause fermentation, followed by a separation process of separating out only said green coffee beans that have passed through the fermentation process.