Citrus pectin is known to influence carotenoid bioaccessibility and absorption in humans, but limited attention has been given to the influence of pectin structure related to the particle size from differentially processed citrus food matrices. In this context, this study aims to investigate the nutritional health benefits of an innovative Citrus clementina concentrate, which is a new citrus-based food made by cross-flow microfiltration. This concentrated citrus-based food was selectively enriched 8-fold in β-cryptoxanthin (43–55 μg g−1) and β-carotene (6–9 μg g−1) as well as 6-fold in pectin (376–462 mg per 100 g). The bioaccessibility of pro-vitamin A carotenoids from commercial and fresh clementina juices versus their concentrates was assessed, including the intestinal carotenoid uptake by Caco-2 cells. Differences in particles size and pectin status resulted in a 7-fold increase in the bioaccessibility of carotenoids in industrial products versus fresh products while limiting their cellular uptake in correlation with larger micelle sizes (10.6 nm and 6.82 nm for industrial and fresh concentrates, respectively). Overall, the highest carotenoid bioaccessibility from industrial concentrate was sufficient to offset the lower carotenoid intestinal uptake related to micelle size. This study highlights that the structure of pectins, more specifically their degree of methoxylation, favors carotenoid bioaccessibility but impairs the intestinal absorption of carotenoids from citrus concentrates.