Citrus greening disease (CGD), devastating phloem residing proteobacteria, Candidatus Liberibacter asiaticus, has significantly impacted various citrus species in Tamil Nadu, India. A roving survey of citrus species revealed that the infected Citrus aurantifolia from Palamedu, Madurai district, exhibited the highest susceptibility, with a disease incidence (DI) of 67.89 % and disease severity (DS) of 65.89 %. In contrast, Poncirus trifoliata from Thadiyankudisai, Dindigul district, demonstrated the highest tolerance with a DI of 10.46 % and DS of 12.56 %. Molecular assessments using PCR and LAMP techniques confirmed the infection of CGD in symptomatic samples of Citrus aurantifolia, Citrus reticulata and Citrus × limonia, while asymptomatic samples tested negative. Biochemical analyses revealed substantial changes in metabolite compositions due to infection. Healthy acid lime contained 79 metabolites, with organic acids (27.84 %) and sugars (20.25 %) being the most dominant groups, whereas infected samples showed reduced diversity with only 60 metabolites. Similarly, healthy mandarin orange contained 93 metabolites, while infected samples exhibited 68 metabolites, significantly reducing sugars and organic acids. Poncirus and Rangpur lime also demonstrated metabolic shifts under infection, reducing the number and proportion of various metabolites. Comparative metabolic analysis highlighted the changes in key metabolites, with significant upregulation of mannose, hexadecenoic acid and maltose in healthy acid lime and downregulation of talose and shikimic acid in infected samples. Metabolomics revealed that compounds like tetramethoxyflavone, quinic acid and linoleic acid were consistently more abundant in healthy citrus samples. These findings provide insights into the biochemical responses of different citrus species to CGD, emphasizing the potential of tolerant varieties such as Poncirus trifoliata and guiding future disease management strategies through targeted metabolomic interventions.