The role of mitochondria in health and disease has dramatically changed in the last decade. Its complex integration into cell physiology is comprised of key metabolic functions of great importance in health maintenance. Treating obesity seems to improve overall mitochondria tissue malfunction; however, the extent of their impact on patients remains elusive due to the lack of follow-up studies. It has been observed that procedures such as bariatric surgery (BS) can modify how our body absorbs nutrients, influencing metabolic processes and mitochondrial function in several cells and tissues. In fact, tissue analysis performed in vivo and in patients support that BS mitigates mitochondrial dysfunction in obese subjects. BS has been observed to reduce the presence of comorbidities such as type 2 diabetes (T2D) and hypertension (HTN) in patients. It is still unclear how BS specifically affects mitochondrial dynamics in obesity-induced comorbidities such as kidney disease. This article provides insightful information regarding the amelioration of mitochondrial dynamics in renal cells and systems after BS. Understanding the multiple pathways that lead to mitochondrial dysregulation in obesity-related kidney disease and relating them to the positive molecular changes after BS may lead to the development of adjuvant therapies to control this and other conditions with similar pathophysiological backgrounds.