Elimination of myeloid leukemia cell 1 (Mcl-1) is an early event in the onset of cell death following DNA damage and, in many settings, plays a critical role in dictating the success of chemotherapeutic agents. Following DNA damage, Mcl-1 is rapidly and efficiently targeted to the 26S proteasome through the action of E3 ubiquitin ligases. Tumors having acquired lesions that lead to stabilization of Mcl-1 are highly aggressive and have a poorer prognosis. Herein, we further characterize an additional mechanism of Mcl-1 proteolysis that is proteasome-independent but mitochondrial-dependent. A mitochondrial targeting signal located in the N terminus of Mcl-1 is essential for targeting Mcl-1 to this alternative degradative avenue. We demonstrate that the Akt/mTORC1 survival pathway protects Mcl-1 from mitochondrial-dependent proteolysis. Disrupting Mcl-1 inner mitochondrial targeting improves the pro-survival capacity of Mcl-1 both ex vivo and in vivo in the well-characterized mouse Eμ-Myc lymphoma model. Our data uncover an important relationship between the mitochondria and the Mcl-1 N terminus in dictating cell fate following DNA damage.