Husk tomato (Physalis ixocarpa Brot. ex. Horm) is mainly used in the preparation of many Mexican sauces due to its unique and slightly acidic flavor, both in raw and cooked forms. These sauces also usually contain Serrano hot pepper (Capsicum annuum L), onion (Allium cepa L.), garlic (Allium sativum L.), coriander (Coriandrum sativum L.) and salt. Mexican sauces are a pre-Hispanic staple food, yet there is scarce knowledge on the phenolic compounds (PC) that reach the colon bound to the indigestible fraction (IF) after intestinal digestion. Thus, the aim of the present work was to evaluate the indigestible fraction of two types of Mexican sauces made with cooked and raw husk tomato: cooked green sauce (CGS) and raw green sauce (RGS). IF of CGS and RGS were fermented in the in vitro model of the human colon (TIM-2) to investigate the PC bioconversion by the gut microbiota after 24, 48 and 72 h. PC of the original sauces and their predigested fractions, as well as the formed metabolites were identified and monitored by HPLC-ESI-QToF-MS. Cooking husk tomato significantly increased the total indigestible fraction (TIF), mainly due to its insoluble indigestible fraction (IIF), and diminished PC. Flavonoids (flavonols and flavones) were the most abundant phenolic group in digested sauces followed by capsaicinoids (a characteristic group derived from hot pepper), hydroxycinnamic acids, and hydroxybenzoic acids. The metabolites 3-(ρ-hydroxyphenyl) propionic acid, 3-(3-hydroxyphenyl) propionic acid and 4-hydroxyphenylacetic acid were the most abundant colonic metabolites identified, which are thought to be derived from the biotransformation of flavonoids and hydroxycinnamates. These results are the first obtained on in vitro colonic fermentation of Mexican sauces and should be considered in future studies on the health effects related to consuming this staple food.