The economic impact of grapevine trunk diseases (GTDs) is increasing worldwide, due to the lack of efficient and simple control protocols for these disease complexes. Possible and efficient GTD management strategies must consider the complexity of host physiological alterations affecting metabolism and defense responses determined by GTD pathogens, and linked to disease expression. In this complexity, the use of biocontrol agents could give advantages in GTD control methods. The effect of the potential biocontrol agent (BCA) Fusarium proliferatum was evaluated using in vitro tests and in dual inoculation with the Botryosphaeria dieback agent Neofusicoc-cum parvum in planta. Artificial inoculations were performed in greenhouse and vineyard experiments at three key vine growth stages, the onset of G (separated clusters), I (flowering) or M (veraison) stages. The biocontrol potential was assessed using pathogenicity tests and transcriptomic analyses. Results showed that the F. proliferatum has potential for phytoprotection, with disease control efficiency related to host plant growth stage. Flowering was confirmed as the growth stage when disease control was least, and efficiency of activated defense responses against pathogen infection was minimum.