The present invention relates to a method of making coffee via germination and fermentation, and a coffee beverage. Fruits or natural medicinal materials are added in secondary fermentation to enhance or add flavors. Specifically, the present invention relates to a method of making coffee by germinating and fermenting coffee green beans with beneficial microorganisms, in which the coffee green beans are germinated and fermented in multiple steps by adding fruits or natural medicinal materials to a culture fluid, wherein the culture fluid contains rice water containing sea salt, sugars, low-fat milk, and brown rice husk powder Bacillus natto extracted from soybean paste and a mixture of beneficial microorganisms such as Bacillus subtilis, lactic acid bacteria, and yeast. According to the method of the present invention, harmful components of coffee are reduced and beneficial components thereof are enhanced and added. Secondary fermentation of coffee green beans proposed in the present invention is characterized in that due to its particular temperature and duration, the fruits or natural medicinal materials added in the secondary fermentation of coffee green beans, such as strawberry, banana, pineapple, blueberry, cherry, grapes, apple, pear, ginger, Angelica gigas, and lemon myrtle are optimally aged and fermented, and thus, the method of the present invention has the potential of providing novel items differentiated from commonplace items currently on the menu at most coffee shops. Additionally, coffee extracts produced by germinating and fermenting coffee green beans by using the mixture of beneficial microorganisms of the present invention can be applied to soaps, cleansers, cosmetics, and health foods as effective components.COPYRIGHT KIPO 2017본 발명은 2차 발효 시에 과일이나 천연물 약재 등을 첨가함으로써, 맛을 증진 및 추가시킬 수 있는 발아 발효 커피의 제조방법 및 커피 음료에 대한 것으로서, 쌀뜨물에 천일염, 당, 저지방 우유, 현미껍질가루를 넣고 청국장에서 추출한 바실러스 낫토(Bacillus natto)외 고초균, 유산균, 효모 등 복합 유용미생물을 넣은 배양액에 과일 또는 천연물 약재를 첨가하여 커피의 생두를 다단 발아
