DRIFT, HPLC-MS, and SPME-GC/MS analyses were used to unveil the structure and the main functional compounds of red (blood) orange (Citrus sinensis) and bitter orange (Citrus aurantium). The IntegroPectin samples show evidence that these new citrus pectins are comprised of pectin rich in RG-I hairy regions functionalized with citrus biophenols, chiefly flavonoids and volatile molecules, mostly terpenes. Remarkably, IntegroPectin from the peel of fresh bitter oranges is the first high methoxyl citrus pectin extracted via hydrodynamic cavitation, whereas the red orange IntegroPectin is a low methoxyl pectin. C. aurantium IntegroPectin has a uniquely high concentration of adsorbed flavonoids, especially the flavanone glycosides hesperidin, naringin, and eriocitrin.