Mitochondria display key cellular functions, such as respiration, oxidative metabolism, calcium homeostasis, lipid metabolism, antiviral signaling, senescence and apoptosis. Therefore, the control of mitochondrial biology is a crucial aspect for cellular homeostasis. In the last years, a substantial amount of evidence have turned mitochondrial dynamics into a key aspect of mitochondrial biology, not only by controlling mitochondrial metabolism, but also by preserving mitochondrial quality. Dysregulation of mitochondrial dynamics is found in a variety of pathologies. Moreover, alterations in mitochondrial dynamics proteins lead to mitochondrial abnormalities, characterized by accumulation of damaged and dysfunctional mitochondria, which are involved in neurodegenerative diseases, muscle atrophy, sarcopenia, aging and metabolic diseases such as type 2 diabetes or obesity. In this review, we will focus on how mitochondrial dynamics, by controlling mitochondrial function and quality, has emerged as a regulator of metabolic homeostasis, and how its dysregulation is involved in the development of metabolic diseases.