Because of the relevant effects of plant-derived polyphenols (PP) on monogastrics and ruminants’ nutrition, emissions and performance, an increasing number of in vivo and in vitro studies are being performed to better understand the mechanisms of action of polyphenols at both the ruminal and intestinal levels. The biological properties of these phenolic compounds strongly depend on their degradation, absorption and metabolism. The harmonized in vitro digestion method (INFOGEST) is one of the most reliable in vitro methods used to assess the bioaccessibility and or antioxidant activity of PP contained in different matrixes, as well as the interactions of PP and their degradation products with other feed ingredients. The effects of PP released from their matrix after in vitro digestion on different intestinal physiological parameters, such as epithelium integrity, can be further evaluated by the use of ex vivo models such as the Ussing chamber. This review aims to describe the combination of the INFOGEST method, coupled with the Ussing chamber as a valuable model for the digestion and subsequent effects and absorption of phenolic compounds in monogastrics and potentially in ruminants. The advances, challenges and limits of this approach are also discussed.