Cereulide (CER) intoxication occurs at relatively high doses of 8 µg/kg body weight. Recent research demonstrated a wide prevalence of low concentrations of cereulide in rice and pasta dishes. However, the impact of an exposure to low doses of cereulide was never studied before. In this research, we investigate the effect of low concentrations of cereulide on the behavior of intestinal cells using Caco-2 cell line. The MTT (mitochondrial 3-(4, 5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) and the SRB (Sulforhodamine B) reactions were used to measure the mitochondrial activity and the measurement of cellular protein content, respectively. Both assays showed that differentiated Caco-2 cells were sensitive to low concentrations of CER (in MTT reaction 1 ng/mL after 3 days of treatment ; in SRB reaction 0.125 ng/mL after 3 days of treatment). Cell counts revealed that cells were released from the differentiated monolayer at 0.5 ng/mL of cereulide. Additionally, 0.5 and 2 ng/mL of CER increased lactate presence in the cell culture medium. Proteomic data showed that cereulide at concentration of 1 ng/mL led towards a significant decrease in energy managing and H2O2 detoxification proteins and to an increase in cell death markers. This is amongst first reports to describe the influence of sub-emetic concentrations of cereulide on a differentiated intestinal monolayer model showing that low doses may induce an altered enterocyte metabolism and membrane integrity.