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A previous study using healthy “Valencia” orange fruit found that juicing extraction methods dramatically changed the orange juice (OJ) flavor and phytochemical profiles. The present study was conducted to confirm whether the same changes occur when Huanglongbing (HLB)-affected oranges were used. HLB has extensively spread to most OJ processing regions around the world, substantially deteriorating fruit and juice flavor quality and altering the phytochemical profiles. In this study, the effect of two major juice extractor types, a shear force extractor (SFE) and a reamer extractor (RE), on the juice quality and physiochemical profile was assessed using HLB-affected orange fruit. Juice extracted via SFE resulted in a lower yield with lower peel oil and higher pellet (peel tissue particles) content compared to juice obtained via RE. The SFE juice also had higher levels of hesperidin and other flavonoid glycosides, mainly due to plentiful peel tissue particles. The SFE juice was also abundant in carotenoids due to a large amount of flavedo particles in the juice. On the other hand, polymethoxylated flavones occurred at higher concentrations in the RE juice, and this may be due to the higher peel oil content in this juice. The SFE juice was rich in flavonoid glycosides and carotenoids, which are associated with potential antioxidant properties; however, the extra portion of the phytonutrients mostly existed in the pellets and possibly had low bioavailability. The results obtained from the HLB-affected oranges are in agreement with the previous observations of healthy oranges. Full article