Management of Botrytis bunch rot of grapes often fails in growing seasons when wet weather occurs close to harvest. The absence of fungicide registration post-veraison for grapes destined for export wine further hampers effective disease control. Understanding how much Botrytis can be tolerated in a batch of grapes before a negative impact on wine quality arises can assist grape growers to make disease management decisions. To determine thresholds for bunch rot contamination, Chardonnay grape bunches from a commercial vineyard were divided in to one of five groups and scored for grey mould infection using a scale of 0 to 4 based on visual assessment. Fungal biomass of each group was determined as a function of ergosterol content using HPLC and grapes were vinified in triplicate. Grey mould infection resulted in elevated levels of 1-octen-3-ol, 1-octen-3-one and 3-octanone, compounds associated with earthy mouldy aromas. Using untargeted GC/MS analysis, increasing levels of a number of unidentified sesquiterpenes and 2,3-dimethylnaphthalene were found in grape juice with increasing infection. Levels of hexenal and other C6 compounds were diminished in Botrytis infected fruit, possibly due to degradation of wax layers on the berry surface following fungal colonisation. Sensory analysis indicated wine made from grapes with ≥ 1.05g of dry weight of fungus / kg wet weight of grapes was notably different from wine made with uninfected grapes. Participants couldn’t differentiate between wine made with 0.35g dry weight of fungus / kg wet weight of grapes from unaffected wine, suggesting that the threshold for Botrytis contamination is somewhere in the 0.35 to 1.05g dry weight / kg of grapes range. The findings have implications for Botrytis management decisions around disease control and thresholds for fruit rejection.