Onion basal rot, a serious and persistent disease problem caused by Fusarium proliferatum, results in severe yield reductions, impacting both quantity and quality of onion worldwide. Fusarium proliferatum penetrates roots leading to decay and wilting of the onion plant. It is important to manage this disease to minimize its effects. Here, we investigated the bioactivity of co-culture extract of Aspergillus ochraceus-F. proliferatum (AF) against F. proliferatum responsible for Fusarium basal rot (FBR) in a greenhouse experiment. The results demonstrated that the AF co-culture extract treatment reduced the percentage of infected plants to 0% and significantly enhanced all growth parameters in infected onion plants. Moreover, the treatment with AF co-culture extract performed the highest values in infected onion plant with total pigments of 3.24 mg/g, carbohydrates of 48.95 mg/g, proteins of 105.23 mg/g, phenolics of 41.64 mg/g, and flavonoids of 8.03 mg/g compared with monocultures extracts and chemical fungicide treatments, and healthy control plant. This establishes that fungal co-cultures bioagents represent a promising prospect as substitutes to chemical fungicides beside ameliorating plant growth.