Autophagy is mainly a cellular recycling process that promotes survival, but it can also cause cell death if cell injury persists. The role of mitophagy in tumorigenesis remains uncertain. Other cell death types, such as apoptosis or necrosis, are often altered during tumor development and therefore are not ideal targets to generate efficient antitumor therapies. We have used the system linamarase/linamarin/glucose oxidase (lis/lin/GO) to eliminate tumor cells. This therapeutic strategy is based on the combination of cyanide and oxidative stress to abrogate tumor growth. After severe mitochondrial insult by lis/lin/GO, the electron transport chain is blocked and hydrogen peroxide production increased. This triggers a degradative phase of these damaged organelles inducing mitophagy that finally leads to cell death. This death process depends on the vacuole generation, BNIp3 and the formation of autolysosomes. Importantly, evasion of apoptosis is known to result in resistance to anti-cancer therapies but this inhibition also augments sensitivity to autophagy, which could be used to promote tumor regression. We explored the potential of this powerful mitophagy-inducing system in vitro and in vivo to eradicate human malignant tumors.