Plants in various republics of the world face many dangers, including diseases that threaten crop productivity. The development and increase of novel species of infectious pathogens have made plant growth threatened. Fusarium wilt is one of the fiercest diseases affecting vegetables, which causes a great loss in the quality and quantity of pepper plants all over the world. In this study, stimulation of physiological immune responses in pepper plant using ecofriendly inducers (Aspergillus alabamensis, Aspergillus oryzae, and Aspergillus tubingensis) against Fusarium wilt had been studied. Endophytic fungi were assayed for their capability to synthesize hydrocyanic acid, phosphate solubilization, siderophores, and indole acetic acid synthesis, and the antifungal potential of ecofriendly inducers against F. oxysporum was also examined. A notable antifungal potential antifusarial with a supreme activity of A. tubingensis was found. More ultrastructure by TEM of Fusarium showed that sharp changes occurred in the cell wall, mycelium, and conidia as a result of treatment with A. tubingensis, A. oryzae, and A. alabamensis. The results demonstrated the high severity of F. oxysporum on pepper seedlings. Infected seedlings showed a high reduction in all vegetative parameters, photosynthesis, entire protein, and total carbohydrate. In the current study, the potential of endophytic fungi through foliar and soil application was applied to the Fusarium-infected pepper plants under pot conditions. Disease index, vegetative growth, photosynthetic pigments, osmolyte content, stress markers, and antioxidant isozymes were assessed. The achieved result indicates that tested endophytes through two modes (foliar and soil) lowered PDI and produced high protection, with the most protection influence represented by A. tubingensis (through the soil) by 83.33%. It was concluded that use of A. tubingensis, A. alabamensis, and A. oryzae could be commercially used as eco-friendly agents for the defense of pepper seedlings against Fusarium wilt disease.