Disclosed is a method for manufacturing coffee beans, in which coffee beans are naturally aged by ingredients of natural royal jelly as the coffee beans absorb main ingredients of the natural royal jelly in a natural beehive. According to the present invention, the method comprises the following steps: (a) preparing natural royal jelly in a queen cell inside a beehive with bees; (b) inserting coffee beans into the natural royal jelly in the queen cell inside the beehive with the bees of the step (a); (c) allowing the coffee beans inserted in the natural royal jelly in the queen cell of the step (b) to absorb the natural royal jelly to be aged; (d) inserting the coffee beans of the step (c) in the beehive with the queen cell; (e) allowing the bees to autonomously apply natural enzymes and natural propolis on the coffee beans of the step (d) inserted in the queen cell; and (f) taking out the coffee beans of the step (e), which are naturally aged while the bees autonomously apply the natural enzymes and natural propolis on the coffee beans, from the beehive. According to the present invention, the main ingredients of natural royal jelly in a natural beehive are absorbed by coffee beans so that the coffee beans naturally aged with natural royal jelly ingredients, and thus coffee beans containing beneficial functional ingredients of natural royal jelly, which are known to have a health promotion effect, can be acquired. COPYRIGHT KIPO 2022