Soil-borne diseases in shallots are the main diseases that can cause weight loss, especially for seeds. One of the biological agents that can control the disease is Trichoderma sp. So far, the use of Trichoderma often does not seem effective because the application time is not right. Trichoderma already exists and grows outside and inside plant tissues. This is due to the nature and character of Trichoderma for its antagonistic fungus that competent to colonize the rhizosphere quickly and protect roots from pathogen attack. This study aims to determine the interaction between the application time of Trichoderma sp and varieties on growth and disease development for seed production. The research was carried out at the Margahayu Experimental Garden, Institute Vegetable Research Indonesian (1,250 m.asl), from September to December 2021. The experiment used was a factorial randomized block with two factors and three replications. The first factor is the time of application of Trichoderma (without Trichoderma, before planting, before planting + 2 weeks after planting, and before planting + 2, 4 weeks after planting). The second factor is several varieties of shallots (Violetta, Ambassador, Maja Cipanas, Bima and Trisula). The results showed that there was no interaction between application time and variety on growth, disease attack, and yield of shallot bulbs for seed. However, application time and varieties affected the intensity of the disease of Stemphylium vesicarium and Peronospora destructor. Maja Cipanas showed the highest plant growth (plant height, number of leaves and number of tillers) with dry weight, weight of one month of storage and weight of two months of storage per clump each of 60.19 g; 50.27 g and 39.49 g.