Background: Inflammatory bowel disease (IBD), including Crohn's disease and ulcerative colitis, affects not only the quality of life of patients but also the economy. Therefore, the pathophysiology of IBD and its molecular and cellular mechanisms must be understood in addition to developing therapies to control disease progression. Since mitochondria have been implicated in IBD, mitochondrial biology may be crucial. In this review, we aim to present the current knowledge about mitochondrial role in IBD, and how this knowledge may contribute to the design of new therapies targeting different disease mechanisms. Methods: The search was performed on PubMed on 5 September 2024. The PRISMA checklist was utilized to evaluate the methodological quality of the selected studies. Results: The search yielded 523 articles. The results were further evaluated for inclusion. Reviews, editorials/comments or meeting reports, as well as articles in languages other than English were discarded, then articles whose topic wasn’t relevant to this review were discarded after reading the abstract or whole article. Finally, a total of 52 articles were used for the generation of this review. The latest data finds a nexus of genetic predisposition, microbial and environmental factors, and an altered immune response to be responsible for the development of IBD. Most importantly, the involvement of mitochondria in each of these factors indicates a role for mitochondrial dysfunction in IBD pathogenesis. Mitochondrial alterations are detected in many animal models of IBD and in human tissue samples. Many mutations in genes involved in mitochondrial structure and function have been experimentally proven to induce IBD. Dysfunctional mitochondria also influence the production of cytokines, which in turn affect the course of the disease. Conclusion: The maintenance of mitochondrial function is necessary for a stable immune system. Mitochondrial dysfunction leads to the excessive activation of multiple inflammatory signaling pathways, leading to IBD.