The fungus Gnomoniopsis castaneae is the causal agent of the “brown rot” of sweet chestnut fruits. These days, this pathogen represents one of the main limiting factors for the sustainability of fruit production worldwide. Although heat treatment post-harvest is efficient in completely inactivating the pathogen, the application of appropriate protocols to control “brown rot” in chestnut orchards is required to help in reducing the latent population of the fungus in fruit tissues, and the consequent development of “brown rot” symptoms in the field before the post-harvest handling process. The present study aims to evaluate and compare the efficiency of products at a minimum environmental impact in experimental trials conducted in chestnut orchards in Central Italy for two consecutive years in 2019 and 2020. Phosphonate-based salts and, specifically, Zn-phosphonate were efficient in reducing the impact of the disease and the pathogen inoculum in fruits with an efficacy comparable to the fungicide Tebuconazole. A unique treatment at the blooming time produced the best results for both Zn-phosphonate and Tebuconazole, also giving indirect evidence of female flowers as a main site of infection. Phosphonate salts, and at first Zn-phosphonate, are highly effective to protect chestnut fruits from the ‘brown rot’ fungus G. castaneae. Its use in orchard management may complement the post-harvest heat treatment during the processing of fruits. Although a still ongoing debate on phosphonate salts use and efficacy in agriculture, they can be considered an optimal fungicide in chestnut orchards because of the low environmental impact when used at the recommended doses, the high translocability and stability, and the multiple mechanisms of action.