The occurrence of grapevine trunk diseases (GTDs) increases gradually within vineyards, leading to important economic losses. Several factors could affect grapevine susceptibility to GTDs, especially climate, vine age, soil fertilization, and also rootstock, cultivar and clone. For a cultivar, the level of disease expression can vary with region and from year to year. In this context, our objective was to assess if the expression of esca disease, one of the most widespread GTDs, was also clone-dependent. Two clones (76 and 95) of the “Chardonnay” cultivar, grown in the same plot, were compared according to their developmental and physiological traits, metabolome, and esca foliar symptom expression. Agronomical data and symptom expression were recorded during summer 2015, and metabolome analyses were performed in leaf samples collected from visually healthy vines as control (C), and from both symptomatic (D+) and asymptomatic (D-) shoots of esca-affected vines. The bud burst percentage and the fertility ratio were significantly lower for clone 76 than for clone 95, whereas the plant vigor was similar. The percentage of vines expressing the apoplectic and chronic forms of esca disease was low but slightly higher for clone 95. Global GC-MS analysis highlighted a clone-dependent metabolic fingerprint of disease expression. Additional targeted HPLC analyses showed opposite variations in the accumulation of trans-caffeoyltartaric acid, quercetin-O-glucoside, quercetin-O-galactoside, and kaempferol-O-glucoside (higher levels in control leaves of clone 76 than in diseased ones, and the opposite for clone 95). An original approach, 3D fluorescent analysis, was also used to compare samples and also pointed out significant differences in disease expression between clones. Altogether, this study highlights a clone-dependent metabolic response related to esca-disease expression, and the potential of the 3D fluorescence analysis as a new method to detect it. It would be interesting to extend the analysis to other clones and varieties.