The present invention relates to a method for preparing functional colored fermented lotus roots using natural fermented compositions and colored fermented lotus roots prepared by the same, and more specifically, to a method for preparing functional colored fermented lotus roots using natural fermented compositions including the steps of: (a) slicing the lotus roots; (b) mixing the lotus roots sliced in step (a) with vinegar and washing the lotus roots with water; (c) immersing the lotus roots washed in step (b) in a natural fermentation solution at 25 to 30C for four to ten hours to be fermented and colored. The natural fermentation solution is prepared by the steps of: selecting natural materials; acquiring fresh juice by extracting juice from the selected natural materials or acquiring powder by freeze-drying the selected natural materials; obtaining a mixture by mixing the acquired fresh juice or freeze-dried powder with a fermentation agent containing one or both of yeast and lactobacillus; obtaining a fermented liquid by fermenting the mixture at 20 to 30C for 10 to 30 hours; obtaining a filtrate by filtering the fermented liquid; obtaining a mixture by mixing the filtrate with the fresh juice or the freeze-dried powder; and ripening the mixture at 1 to 10C for 10 to 30 hours. The natural materials include at least one of turmeric, gardenia seeds, beets, aronia, purple sweet potatoes, red rice yeast, schizandra, green teas, chlorella, mulberry leaves, houttuynia cordata, and paprika. According to the present invention, the colored fermented lotus roots prepared by the method can have good quality, superior functionality and storability, and rich nutrients.본 발명은 천연 발효액을 이용한 기능성 착색 발효 연근의 제조방법 및 그 착색 발효 연근에 관한 것으로, 더욱 상세하게는 (a) 연근을 슬라이스하는 단계와, (b) 상기 (a) 단계의 슬라이스된 연근을 식초와 혼합한 후, 물로 세척하는 단계와, (c) 상기 (b) 단계의 세척된 연근을 천연 발효액에 침지시켜 25~30℃에서 4~10시간 동안 발효 및 착색하는 단계를 포함하며, 상기 천연 발효액은 천연재를 선택하는 과정과, 상기 선택된 천연재를 착즙하여 생즙을 수득하거나, 상기 선택된 천연재를 동결건조하여 분말을 수득하는 과정과, 상기 수득된 생즙 또