Fungal infections represent a relevant issue in agri-food and biomedical fields because they could compromise quality of food and humans’ health. Natural extracts represent a safe alternative to synthetic fungicides and in the green chemistry and circular economy scenario, agro-industrial wastes and by-products offer an eco-friendly source of bioactive natural compounds. In this paper, phenolic-rich extracts fromOlea europaeaL. de-oiled pomace,Castanea sativaMill. wood,Punica granatumL. peel, andVitis viniferaL. pomace and seeds were characterized by HPLC-MS-DAD analysis. Finally, these extracts were tested as antimicrobial agents against pathogenic filamentous fungi and dermatophytes such asAspergillus brasiliensis,Alternariasp.,Rhizopus stolonifer, andTrichophyton interdigitale. The experimental results evidenced that all extracts exhibited a significant growth inhibition forTrichophyton interdigitale.Punica granatumL.,Castanea sativaMill., andVitis viniferaL. extracts showed a high activity againstAlternariasp. andRhizopus stolonifer. These data are promising for the potential applications of some of these extracts as antifungal agents in the food and biomedical fields.