The present invention relates to a method for preparing a natural fermentation composition, comprising: a primary fermentation step of mixing bean sprouts, water and a strain, and fermenting same at 50 to 65 ℃ for 15 to 30 days to obtain a primary fermentation product; and a secondary fermentation step of fermenting the primary fermentation product under conditions of a temperature of 15 to 32 °C and a dissolved oxygen concentration of 0.04 to 0.4 mg/L, and then terminating the fermentation when the chemical oxygen demand is 250 to 680 ml/L, to obtain a secondary fermentation product, and allows glutathione to be produced by fermenting bean sprouts under optimized fermentation conditions and enables provision of a fermentation product enabling active ingredients such as vitamins, minerals and phytochemicals retained in natural products to be simultaneously ingested.