High-pressure treatments combined with crossflow microfiltration were used to obtain citrus concentrates enriched in carotenoids. The aim of this study was to investigate the effect of this process combination on carotenoid bioaccessibility and uptake by intestinal Caco-2 cells. Two high-pressure processes, high hydrostatic pressure treatment (HHP) and ultra-high-pressure homogenization (UHPH) were compared to conventional pasteurization. Processing effects on carotenoid content and bioaccessibility, on physicochemical and structural characteristics of the product, on methylation degree of pectins and micelle size after in vitro digestion were assessed. UHPH at 400 MPa drastically enhanced carotenoid bioaccessibility compared to HHP and pasteurization. Moreover, carotenoid uptake by Caco-2 cells was significantly improved by UHPH underlining the importance of the micelle size after in vitro digestion and the degree of methylation of pectins in this uptake. Finally, the in vitro bioavailable carotenoid content of different concentrates was evaluated, taking into account carotenoid content, bioaccessibility and uptake. Combining crossflow microfiltration with UHPH increased by 4–6 fold the bioavailable carotenoid content in the final product. The process led to a concentrate of high nutritional quality compared to the original juice, raw or pasteurized concentrates.