BACKGROUNDCrop quality, yield and farmer income are reduced by soil‐borne diseases, nematodes and weeds, although these can be controlled by allyl isothiocyanate (AITC), a plant‐derived soil fumigant. However, its efficacy against soil‐borne pathogens varies, mainly because of its chemical instability and uneven distribution in the soil. Formulation modification is an effective way to optimize pesticide application. We encapsulated AITC in modified diatomite granules (GR) and measured the formulation's loading content and stability, environmental fate and efficacy against soil‐borne pathogens, and its impact on the growth and yield of tomatoes.RESULTSWe observed that an AITC loading content in the granules of 27.6% resulted in a degradation half‐life of GR that was 1.94 times longer than 20% AITC emulsifiable concentrate in water (EW) and shorter than AITC technical (TC) grade. The stable and more even distribution of GR in soil resulted in relatively consistent and acceptable control of soil‐borne pathogens. Soil containing AITC residues that remained 10–24 days after GR fumigation were not phytotoxic to cucumber seeds. GR significantly reduced soil‐borne pest populations, and tomato growth and yield increased as AITC dosage increased. GR containing an AITC dose of 20 g m−2 effectively controlled pathogens in soil for about 7 months and improved tomato yield by 108%.CONCLUSIONOur research demonstrates the benefits of soil fumigation with loaded AITC over other formulations for effective pest control, and improved tomato plant growth and fruit yield. Fumigant encapsulation appears to be a useful method to improve pest and disease control, environmental performance and fumigant commercial sustainability. © 2024 Society of Chemical Industry.