Understanding the residue fates of chlorothalonil, chlorfenapyr and difenoconazole in chilli peppers is essential for safeguarding food safety and human health. Here, the dissipation, removal and risk assessment of chlorothalonil, chlorfenapyr and difenoconazole in chilli peppers from field to table were systematically investigated. In field trials, the dissipation of chlorothalonil, chlorfenapyr and difenoconazole followed the first-order kinetics in chilli peppers, with half-lives of 6.80, 9.00 and 21.00 days, respectively. Residues of the metabolites, including 4-hydroxychlorothalonil (SDS-3701), tralopyril and difenoconazole–alcohol (CGA205375), were also detected in chilli peppers. The processing factors (PFs) in pickled chilli and chilli paste for washing, salting and fermentation were <1, with the overall process having PFs of 0.10–0.93. Chronic, acute and cumulative risk assessments indicated that dietary exposure to chlorothalonil, SDS-3701, chlorfenapyr, difenoconazole and CGA205375 was within acceptable limits of chilli pepper consumption. However, the total dietary risk of chlorothalonil and difenoconazole was alarming, with risk quotients (RQs) of 162% and 140%, respectively. The results could guide the safe and reasonable use of chlorothalonil, chlorfenapyr and difenoconazole in agriculture, as well as provide reference for assessing their residue levels in chilli products.