Cold stress is one of the major environmental factors limiting the amount of plant mass for bioenergy production. A chilling-sensitive Jatropha (Jatropha curcas L.) as a bioenergy crop was used to investigate the cold injury process at the physiological and biochemical levels. Various physiological parameters such as leaf length, width, stomatal conductance, chlorophyll fluorescence, and electrolyte leakage were measured to determine the growth rate of leaves cold-treated (7 and 2°C) for 5 days. These parameters of cold-treated Jatropha were significantly reduced from day 1 compared with control (23°C). Using the pH indicator bromocresol purple, it was shown that surface pH of Jatropha root in control was strongly acidified by time only from the starting pH 6, while H⁺-efflux of the surface of cold-treated roots did not change. H⁺- ATPase activity of plasma membrane (PM) isolated from leaves and roots of cold-treated Jatropha was decreased in a time-dependent manner. The expression of PM H⁺-ATPase and 14-3-3 protein, which participates in phosphorylation of PM H⁺-ATPase was reduced in the presence of cold stress. Interestingly, fusicoccin, an activator of the PM H⁺- ATPase, alleviated cold-injury by stimulating the enzyme in leaves. These results may suggest that the activity and expression of PM H⁺-ATPase in Jatropha is closely related to the overcoming of cold stress.