Epithelial to Mesenchymal Transition (EMT), a process involved in organogenesis and wound healing is now at the center stage of cancer metastasis. While most of the current research is focused on defects arising in the nuclear genome, the contribution of defects in mitochondria has remained under investigated. In the past decade, the association between mitochondrial genomic (mtDNA) and functional defects resulting in altered metabolism with tumor progression and poor outcome has become more evident. Here we review the contribution of mitochondria in epithelial-to-mesenchymal transition, particularly focusing on breast cancer. Our goal is to highlight the critical role that mitochondrial genome defects induced retrograde signaling play in driving cellular plasticity. We will further discuss the molecular intermediates of the retrograde signaling pathway, which can potentially be novel therapeutic targets in mitochondrial stress induced EMT.