BACKGROUNDGnomoniopsis smithogilvyi is the major chestnut pathogen, responsible for economic losses and recently described as a 3‐nitropropionic acid and diplodiatoxin mycotoxin producer. Bacillus amyloliquefaciens QST 713 (Serenade® ASO), B. amyloliquefaciens CIMO‐BCA1, and the fungicide Horizon® (tebuconazole) have been shown to reduce the growth of G. smithogilvyi. However, they enhanced mycotoxin production. Proteomics can clarify the mould's physiology and the impact of antifungal agents on the mould's metabolism. Thus, the aim of this study was to assess the impact of Horizon®, Serenade®, and B. amyloliquefaciens CIMO‐BCA1 in the proteome of G. smithogilvyi to unveil their modes of action and decipher why the mould responds by increasing the mycotoxin production. For this, the mycelium close to the inhibition zone provoked by antifungals was macroscopically and microscopically observed. Proteins were extracted and analysed using a Q‐Exactive plus Orbitrap.RESULTSThe results did not elucidate specific proteins involved in the mycotoxin biosynthesis, but these agents provoked different kinds of stress on the mould, mainly affecting the cell wall structures and antioxidant response, which points to the mycotoxins overproduction as a defence mechanism. The biocontrol agent CIMO‐BCA1 acts similar to tebuconazole. The results revealed different responses on the mould's metabolism when co‐cultured with the two B. amyloliquefaciens, showing different modes of action of each bacterium, which opens the possibility of combining both biocontrol strategies.CONCLUSIONThese results unveil different modes of action of the treatments that could help to reduce the use of toxic chemicals to combat plant pathogens worldwide. © 2023 Society of Chemical Industry.