Plant growth and survival depends critically on photo assimilates. Pathogen infection leads to changes in carbohydrate metabolism of plants. In this study, we monitored changes in the carbohydrate metabolism in the grapevine inflorescence and leaves using Botrytis cinerea and Botrytis pseudo cinerea. Fluctuations in gas exchange were correlated with variations in chlorophyll a fluorescence. During infection, the inflorescences showed an increase in net photosynthesis with a stomatal limitation. In leaves, photosynthesis decreased, with a non-stomatal limitation. A decrease in the effective quantum yield (ФPSII) was accompanied by an increase in photochemical (qP) and non-photochemical quenching (qN). The enhancement of qP and ФPSII could explain the observed increase in Pn. In leaves, the significant decline in ФPSII and qP, and increase in qN suggest that energy was mostly oriented towards heat dissipation instead of CO2 fixation. The accumulation of glucose and sucrose in inflorescences and glucose and fructose in the leaves during infection indicate that the plant's carbon metabolism is differently regulated in these two organs. While a strong accumulation of starch was observed at 24 and 48 hpi with both species of Botrytis in the inflorescences, a significant decrease with B. cinerea at 24 hpi and a significant increase with Botrytis pseudo cinerea at 48 hpi were observed in the leaves. Based on these results, it can be said that during pathogen attack, the metabolism of grapevine inflorescence and leaf is modified suggesting distinct mechanisms modifying gas exchange, PSII activity and sugar contents in these two organs.