Gnomoniopsis smithogilvyi (Gs) is a relevant pathogen of chestnut since it provokes significant losses worldwide. The aim of this study was to screen the effect of a new biocontrol agent (BCA) against Gs isolated from chestnut (CIMO-BCA1) on the mould’s growth as well as on the production of secondary metabolites. The chemical fungicide Horizon® (tebuconazole; HOR) and the commercial biofungicide Serenade® ASO (Bacillus amyloliquefaciens QST 713; ASO) were also tested. Three concentrations of each antifungal (HOR, ASO, and CIMO-BCA1) were faced with Gs in the growth study in a chestnut-based medium. The intermediate concentrations were used for the analyses of metabolites by LC-MS/MS. CIMO-BCA1 was also identified as B. amyloliquefaciens. All agents reduced the mould’s growth, and the CIMO-BCA1 treatment with an intermediate concentration was the most effective. The metabolite analysis revealed, for the first time, the production of two mycotoxins by Gs, including 3-nitropropionic acid and diplodiatoxin. Additionally, HOR stimulated the production of diplodiatoxin. In conclusion, Gs could present a health risk for consumers. B. amyloliquefaciens strains effectively decreased the mould’s growth, but they must be applied at effective concentrations or in combination with other strategies to completely reduce the hazard.