Emerging mycotoxins are currently gaining more attention due to their high frequency of contamination in foods and grains. However, most data available in the literature are in vitro, with few in vivo results that prevent establishing their regulation. Beauvericin (BEA), enniatins (ENNs), emodin (EMO), apicidin (API) and aurofusarin (AFN) are emerging mycotoxins frequently found contaminating food and there is growing interest in studying their impact on the liver, a key organ in the metabolization of these components. We used an ex vivo model of precision-cut liver slices (PCLS) to verify morphological and transcriptional changes after acute exposure (4 h) to these mycotoxins. The human liver cell line HepG2 was used for comparison purposes. Most of the emerging mycotoxins were cytotoxic to the cells, except for AFN. In cells, BEA and ENNs were able to increase the expression of genes related to transcription factors, inflammation, and hepatic metabolism. In the explants, only ENN B1 led to significant changes in the morphology and expression of a few genes. Overall, our results demonstrate that BEA, ENNs, and API have the potential to be hepatotoxic.