Large part of the world production of fruit and vegetables is destined for processing by the food industry. This intense process generates tons of by-products which may be sources of fiber and bioactive compounds, as polyphenol and carotenoids. Thus, there is a growing number of studies for the valorization of these by-products focusing on the extraction of bioactive compounds. However, the total amount ingested of bioactive compounds may not reflect the amount available for intestinal absorption, which refers the bioaccessibility of these compounds. In addition, the interaction between bioactive compounds with dietary fiber and other nutrients may influence on their bioaccesiibility and may impair the understanding of the physiological effects of this by-product’s, as prebiotic potential. In this sense, the purpose of this review was to summarize the main results obtained on the bioaccessibility of the two major bioactive compounds of fruit and vegetable by-products, polyphenols and carotenoids, in order to corroborate the biopotential of this food matrix. Additionally, attempt to elucidate the relationship between these by-products’ composition and the emerging prebiotic property reported. In general, the bioaccessibility of polyphenols and carotenoid compounds from fruit and vegetable by-products shows high variability and it is suggested that composition of food matrix is one of the mainly factors for their bioaccessibility. In addition, it is observed a promising prebiotic effect from these by-products and, with this whole matrix as substrate, the prebiotic effect may be a result of the shared action of mainly prebiotic oligo- and polysaccharides and available polyphenols and metabolites.