The liver, skeletal muscle, and adipose tissue are central energy-metabolizing organs and insulin-sensitive tissues, playing a crucial role in maintaining glucose homeostasis. As the powerhouse of the cell, mitochondria not only regulate insulin secretion but also oversee the oxidative phosphorylation and β-oxidation of fatty acids, processes vital for the metabolism of carbohydrates and fats, as well as the synthesis of ATP. The mitochondrial quality control system is of paramount importance for sustaining mitochondrial homeostasis, achieved through mechanisms such as protein homeostasis, mitochondrial dynamics, mitophagy, and biogenesis. Evidence suggests that dysfunctional mitochondria may significantly contribute to insulin resistance and ectopic fat storage in the liver, offering new insights into the strong correlation between mitochondrial dysfunction and the development of obesity, diabetes mellitus type 2 (T2DM), and non-alcoholic fatty liver disease (NAFLD). This manuscript aims to delve into the precise mechanisms by which imbalances in mitochondrial quality control lead to metabolic disorders in the liver, skeletal muscle, and adipose tissue, the 3 major insulin-sensitive organs. In the liver, mitochondrial dysfunction can lead to disturbances in glucose and lipid metabolism, resulting in insulin resistance and fat accumulation—a key factor in the development of NAFLD. In skeletal muscle, reduced mitochondrial function can decrease ATP production, weakening the muscle’s ability to uptake glucose, thereby exacerbating insulin resistance. In adipose tissue, mitochondrial dysfunction can impair adipocyte function, leading to lipotoxicity and inflammatory responses,which further contribute to insulin resistance and the onset of metabolic syndrome. Moreover, the interorgan crosstalk among these 3 tissues is essential for overall metabolic homeostasis. For instance, hepatic gluconeogenesis and glucose utilization in skeletal muscle are both influenced by the health status of their respective mitochondrial populations. The conversion between different types of adipose tissue and the ability to store lipids depend on normal mitochondrial function to avert ectopic fat accumulation in other organs. In summary, this manuscript emphasizes the critical role of mitochondrial quality control in maintaining the metabolic stability of the liver, skeletal muscle, and adipose tissue. It elucidates the specific mechanisms by which mitochondrial dysfunction in these organs contributes to the development of metabolic diseases, providing a foundation for future research and the development of therapeutic strategies targeting mitochondrial dysfunction.