Jatropha, a popular biodiesel crop, suffers severe losses due to Jatropha leaf curl Gujarat virus (JLCuGV) infection in Gujarat (India). Gas chromatography-mass spectrometry (GC-MS) analysis of healthy and infected tissue revealed that the metabolites like sugars, polyols, carboxylic acids, fatty acids, polyphenols, and amino acids were regulated on JLCuGV infection. The sugars (glucose, sucrose, and fructose) increased, while carboxylic acids (malic acid, citric acid and quinic acid) and polyols (galactinol, butanetriol, triethylene glycol, myo-inositol, erythritol) decreased remarkably in infected Jatropha tissue. The increased accumulation of polyphenols in JLCuGV infected tissue suggests activation and involvement of polyphenol biosynthesis pathways as a defence response to geminivirus. All these metabolic variations indicated that sugar metabolism and tricarboxylic acid (TCA) cycle pathways are regulated as a defence response as well as a disease development response to geminivirus infection in Jatropha.