A quantitative risk assessment of mycotoxins due to the consumption of chilli (Capsicum annum L.) and black pepper (Piper nigrum L.) was performed in Sri Lanka. A food frequency questionnaire was administered in order to collect the data on consumption of spices by households in the Northern and Southern region (n = 249). The mean chilli consumption in the North was significantly higher (p < 0.001) compared to the South. Mean exposure to aflatoxin B1 (AFB1) in the North (3.49 ng/kg BW/day) and South (2.13 ng/kg BW/day) have exceeded the tolerable daily intake due to chilli consumption at the lower bound scenario, while exposure to OTA was small. Dietary exposure to other mycotoxins, fumonisin B1, fumonisin B2, sterigmatocystin and citrinin due to spices were estimated. Margin of exposure estimations at the mean exposure to AFB1 were remarkably lower due to chilli (45-78) than for pepper (2315–10,857). Moreover, the hepato cellular carcinoma (HCC) risk associated with the mean AFB1 exposure through chilli at the lower bound was 0.046 and 0.028 HCC cases/year/100,000 based on the North and South consumption, respectively. AFB1 exposure via chilli should be considered as a great public health concern in Sri Lanka due to both high mycotoxin concentration and high consumption.