Intercropping is a tried-and-true approach for restoring depleted agricultural soils, making better use of resources, controlling pests and disease, and ultimately boosting crop yield by reducing soil disease. This study tries to evaluate the role of tomato potato onion intercropping in induction tomato resistance against the soil-borne pathogen, Fusarium oxysporum. The study included four treatments Tomato seedlings monoculture in non-infected soil, Tomato seedlings monoculture in Fusarium infected soil, Tomato/potato onion intercropping in non-infected soil, Tomato/potato onion intercropping in Fusarium infected soil. Roots and shoots of tomato plants and soil were collected at 2 and 4 weeks after transplanting. Results showed that tomato/potato onion intercropping can enhance tomato resistance against Fusarium wilt. This is achieved through the improvement of soil enzymes and antifungal enzyme activity in the soil which release compounds from the Fusarium cell wall hydrolysis which act as elicitors to initiate defense response in the tomato plants. The defense response is represented in the elevation of the antioxidant capacity and enzymes which antagonize the oxidative stress. Additionally, as a result of the defense response, the secondary metabolism has improved, as evidenced by increased activity in the phenylalanine ammonia-lyase and consumption of the shikimic acid, which raises the amounts of phenols and flavonoids. Besides that, the intercropped tomato showed high activity in the antifungal enzymes and high content of cell wall-bound phenols which stop the fungal growth spread inside tomato plants.