This study aimed to describe the effect of storage (raw, 7 and 14 days) and boiling time (raw and 60 minutes) of yacon tubers to short-chain fatty acids (SCFA) and lactic acid concentrations in media supplemented yacon tubers extracts, as fermentation results of Bifidobacteriumlongum Reuter ATCC 15707 and Lactobacillus acidophilus IFO 13951. High-Performance Liquid Chromatography (HPLC) was applied for analysis the concentration of 1) fructooligosaccharide (1-kestosa, nystose, and 1 F -fructofuranosylnystose), saccharides (glucose, fructose, and sucrose) yacon tubers, 2) SCFA (acetic acid, propionic acid, and butiric acid) and lactic acid in fermentation media. Increasing storage and boiling time, would increase of saccharides and decreasefructooligosaccharideconcentrations. In the media supplemented with yacon tubers extracts, Bifidobacteriumlongum Reuter ATCC 15707 produces SCFA and lactic acid higher than Lactobacillus acidophilus IFO 13951. Duration of storage and boiling affects the levels of SCFA-lactic acid. The highest concentrations of SCFA-lactic total on media with supplemented 14 days storage and boiling 60 minutes or raw/fresh yacon tubers extracts.