Flavor perception integrates sensory input from chemical receptors triggered by taste- and aroma-active metabolites to contribute to food flavor quality. Many factors alter flavor quality. Disease affects aroma and flavonoid constituents, causing off-flavors in plants. Huanglongbing (HLB) disease negatively affects citrus, although lemons are more tolerant. Lemon juice quality of HLB-affected fruits is not well studied. Lemon juice aroma-active compounds were profiled in this study using gas chromatography/mass spectrometry-olfactometry, and other metabolites contributing to overall flavor quality were investigated. Lemon juice from different rootstocks was discriminated using the metabolic profile. Flavor and other lemon juice metabolites also distinguished symptomatic from asymptomatic trees. Pathway enrichment analysis demonstrated that biosynthesis pathways of the Phosphotransferase system (PTS), and Starch and sucrose metabolism involving fructose, glucose and sucrose, were highly influenced by HLB status. This study provides the first comprehensive view of lemon juice metabolites, including alterations resulting from rootstock differences or disease severity.