In mammals, cardiac ischemic injury leads to loss of muscle filled in with less functional scar tissue. Direct reprogramming of the cardiac fibroblasts populating a scar to functional cardiomyocytes represents a promising potential treatment for these patients. This reprogramming involves a metabolic shift from the more glycolytic CF state to mitochondrial oxidative phosphorylation in the induced CMs, including increased mitochondrial biogenesis. Various reprogramming strategies make use of agents, which in addition to canonical roles, promote mitochondrial energetics and a dynamic shift towards mitochondrial fusion. We decided to investigate whether these mitochondrial structural and functional shifts might represent a mechanism of reprogramming. We characterized various structural and energetic properties of mitochondria in neonatal CFs, CMs, and at multiple time points during reprogramming. Using the baseline CF and CM mitochondrial data, we built a model to follow cells in pseudotime during reprogramming, and identified a time course for mitochondrial changes. We also investigated whether various mitochondrial perturbations designed to promote these changes might increase reprogramming efficiency. Promotion of mitochondrial fusion activity and biogenesis increased the proportion of reprogrammed cells. Conversely, promotion of fission and inhibitors for electron transport system enzymes inhibited reprogramming.