Polyphenols and carotenoids are known for their positive effects on health, including the prevention of several chronic diseases, and many food materials have been studied so far in order to investigate the content of polyphenols and carotenoids. However, the in vivo effects of these compounds depend not only on their concentrations, but also on their digestion, bioaccessibility and bioavailability after ingestion. Even though the exact amount of bioactive compounds that is absorbed and utilized cannot be predicted, in vitro methods are being utilized widely to understand the fate of these compounds instead of in vivo methods, which have ethical and economical limitations. As a result, several different models have been developed to evaluate the digestion and absorption of polyphenols and carotenoids. Within this chapter, frequently employed models used for studying the digestion, bioaccessibility and colonic fermentation of polyphenols and carotenoids are evaluated. These in vitro models include gastrointestinal digestion (static and dynamic models), cell culture (Caco-2 cell line, HT29 cell line and co-culture models), intestinal tissue (everted sac, Ussing chamber and 3D cultures) and colonic fermentation (SHIME®, TIM-2 and SIMGI®) models. Specific applications for the study of the metabolic fate of non-extractable polyphenols are discussed.