Powdery mildew on Chardonnay grapes resulted in increased levels of a grape thaumatin‐like protein, VvTL2, in the free run juice compared to that from uninfected grapes. These increased levels persisted through winemaking and at the highest level of infection (> 30% of bunches infected) had a significant impact on the haziness in the wine following a heat test. Infection of Cabernet Sauvignon grapes (1–20% of bunches infected) did not affect the protein concentration of free run juice, and only traces of pathogenesis‐related (PR) proteins remained detectable in the Cabernet Sauvignon wines from either infected or healthy grapes. In contrast, infection of Chardonnay or Semillon grapes by Botrytis cinerea in the vineyard resulted in decreased levels of all PR proteins in the free run juice and in a total protein extract from infected berries compared to that from uninfected grapes. Similar trends were observed when B. cinerea was grown in the laboratory on surface‐sterilised berries or in filter‐sterilised juice.