Myeloid cell leukemia-1 (Mcl-1) is an antiapoptotic oncoprotein overexpressed in several malignancies and acts as one of the promising therapeutic targets for cancer. Even though there are several small molecule based Mcl-1 inhibitors reported, the delivery of Mcl-1 inhibitor at the target site is quite challenging. In this regard, we developed a series of mitochondria targeting luminescent cyclometalated iridium(III) prodrugs bearing Mcl-1 inhibitors via ester linkage due to the presence of Mcl-1 protein in the outer mitochondrial membrane. Among the synthesized prodrugs, IrThpy@L2 was found to exhibit the potent cytotoxicity (IC50 = 30.93 nM) against HCT116 cell line when compared with bare Mcl-1 inhibitors (IC50 > 100 μM). Mechanistic studies further revealed that IrThpy@L2 quickly gets internalized inside the mitochondria of HCT116 cells and undergoes activation in the presence of overexpressed esterase which leads to the release of two cytotoxic species i.e. Mcl-1 inhibitors (I-2) and cytotoxic iridium(III) complex (IrThpy@OH). The improved cytotoxicity of IrThpy@L2 is due to the mitochondria targeting ability of iridium(III) prodrug, subsequent esterase activated release of I-2 to inhibit Mcl-1 protein and IrThpy@OH to generate reactive oxygen species (ROS). After prodrug activation, the released cytotoxic species cause mitochondrial membrane depolarization, activate a cascade of mitochondria-mediated cell death events, and arrest the cell cycle in S-phase which leads to apoptosis. The potent anticancer activity of IrThpy@L2 was further evident from the drastic morphological changes, size reduction in the solid tumor mimicking 3D multicellular tumor spheroids (MCTS) of HCT116.