Basal bulb rot (BBR) of shallot caused by Fusarium oxysporum f. sp. cepae is one of the highly deleterious diseases on shallot, Allium cepa L. var ascalonicum Backer. in Indonesia. This study aimed to assess the potency of organic mulch, composted plant residues, and endophytic Trichoderma asperellum to control this disease. Treatment with mulch alone, mulch plus compost, mulch plus T. asperellum, and combination of all the three provided the decrease of BBR incidence by 15%, 20%, 29%, and 39% and the increase of shallot productivity by 22%, 66%, 84%, and 125%, respectively. Observation of another treatment impact on the fungal occurrence at harvest time indicated that their population in soil increased by 671%, 771%, 257%, and 814% and the fungal colonization in root tissues mounted by 31%, 77%, 77%, and 74%, respectively. The introduced Trichoderma was found predominantly, especially in leaf tissues of inoculated shallot. These data showed that all the treatments were able to control BBR disease. However, the most effective was the mulch in combination with compost and T. asperellum. Therefore, large-scale disease control could take advantage of this integration.