Despite the fact that oxidative stress (OS) has been implicated in IBD pathogenesis and mitochondria are the substantial source of ROS, little attention has been paid to these organelles. We hypothesize that OS can lead to mitochondrial dysfunctions recapitulating various IBD abnormalities. The present study will to investigate the impact of OS on mitochondrial antioxidant content, energy production, calcium homeostasis, cell death, transcription factors status and DNA integrity. We used FE/ASC to generate OS in Caco‐2 cells. Our results show that the administration of FE/ASC (0.2 mM/2 mM) (1) increased MDA levels; (2) reduced ATP production; (3) led to alterations in the gene expression and protein mass of mitochondrial transcription factors (mtTFA, mTFB1, mTFB2) without any effects on POLRMT; (4) provoked dysregulation of mitochondrial calcium homeostasis; (5) elicited DNA lesions as illustrated by the raised levels of 8‐OHdG; (6) lowered, OGG1, one of the first lines of defence against 8‐oxodG mutagenicity; and (7) upregulated cytochrome C and AIF protein expressions, indicating exaggerated apoptosis. The presence of the powerful antioxidant BHT prevented the occurrence of OS and most of the mitochondrial abnormalities. In conclusion, our results suggest that OS causes mitochondrial dysfunctions and modulates mitochondrial transcription factors. We believe that the identification of OS‐mediated mitochondrion disorders adds new information regarding their implication in IBD pathogenesis.