Khao-Mak is a traditional dessert from Thailand with a unique flavor profile from low alcohol and lactic acid. Khao-Mak is made from cooked glutinous rice fermented with the starter culture (Look-Pang), Look-Pang including yeast, molds, lactic acid bacteria, and herbs. Khao-Mak is made from white glutinous rice, pigmented rice (Kam-Doi, Leum-Pua), and germinated pigmented rice (Kam-Doi, Leum-Pua). This investigation focused on the physico-chemical, metabolites and flavor profiles of Khao-Mak in the fermentation period to optimize the best time for fermentation and biomarkers. The best time for fermentation was 2 days, because after day 2 of fermentation the physico-chemical properties slightly changed. Leum-Phua is the best rice variety for producing Khao-Mak in this research, because Leum-Phua was found to have the highest total anthocyanin content (TAC), total phenolic content (TPC) and %DPPH. In addition, metabolomics and flavoromics analysis results discovered 37 and 48 compounds, respectively, produced during fermentation processes. The metabolites and flavor compounds found were used to differentiate all samples using principal component analysis (PCA). Khao-Mak had strong alcohol, wine-like, whiskey-like, solvent-like, sweet and fruity flavors. Heat plot of metabolites and flavor compounds showed that lactic acid, acetic acid, 3-methyl-1-butanol, 2-methyl-1-propanol, and 1-propanol were in greater proportions than other compounds and used as biomarkers for fermentation.