Determination of bioactive compounds content directly from foodstuff is not enough for the prediction of potential in vivo effects, as metabolites reaching the blood system may be different from the original compounds found in food, as a result of an intensive metabolism that takes place during absorption. Nutritional efficacy of food products may be ensured by the determination of bioaccessibility, which provides valuable information in order to select the appropriate dosage and source of food matrices. However, between all the methods available, there is a need to establish the best approach for the assessment of specific compounds. Comparison between in vivo and in vitro procedures used to determine bioaccessibility and bioavailability is carried out, taking into account the strengths and limitations of each experimental technique, along with an intensive description of actual approaches applied to assess bioaccessibility of bioactive compounds. Applications of these methods for specific bioactive compound's bioaccessibility or bioavailability are also discussed, considering studies regarding the bioavailability of carotenoids, polyphenolic compounds, glucosinolates, vitamin E, and phytosterols.