Functioning as a pivotal platform for energy production and transduction, mitochondria generate ATP to meet the dynamic demands of embryonic development. Consequently, disruption or alteration in mitochondrial activity influences not only cellular status, but also can impact organ formation. Disrupted mitochondrial performance not only impairs cardiovascular function but can also disrupt cardiac maturation through prevention of the myocardium’s transition between the trabeculation to the compaction phase. During embryonic development, proliferating cardiomyocytes create a trabecular mesh network. Gradual compaction of this network transforms the intra-trabecular spaces into the capillaries of the coronary circulation. Achievement of functional compaction and ultimately normal cardiac function is dependent in part on mitochondrial well-being with failure to complete remodeling of the inner trabecular layer contributing to disrupted endocardial vasculature and fibrosis, left ventricular noncompaction (LVNC). LVNC, commonly associated with mitochondrial genetic alterations, is speculated to occur due to an interruption during the process of compaction at the early developmental stages of the left ventricle (LV). Mitochondrial mutations, remain the common etiology of LVNC with a wide spectrum of these genes associated with other cardiomyopathies related to LVNC. Understanding the impact that mitochondrial genetic alterations have on the evolution of cardiac noncompaction could provide new treatment opportunities.