Dysregulation of mitochondrial functions can significantly disrupt energy metabolism in the myocardium. However, mitochondrial mechanisms of cardioprotection and their disruption in metabolic disorders are still insufficiently studied. The aim of the our work was to characterize mitochondrial mechanisms of cardioprotection in ischemia-reperfusion of the rat heart under conditions of insulin resistance and hypoxic preconditioning. Adult male Wistar rats were induced to insulin resistance by consuming a high-fat diet with 58% fat for 14 days. Hypoxic preconditioning was reproduced by exposure to hypobaric hypoxia (360 Torr) in a pressure chamber for 3 hours. To assess the cardioprotective effects, 30-minute ischemia and 40-minute reperfusion of the isolated heart were simulated after 24 hours with isovolumic retrograde perfusion according to the Langendorff method. The size of the myocardial infarction, oxidative stress indicators and the level of expression of the mitochondrial protein PGC-1α were determined. Mitochondria were examined using electron microscopy. In the myocardium of insulin-resistant rats, there was a quantitative increase in all mitochondrial subpopulations, activation of their intracellular connections with other organelles, and an increase in the level of PGC-1α expression in the left ventricle. At the same time, activation of free radical processes in the myocardium was observed with an increase in the content of TBA-AP and activation of antioxidant mechanisms, in particular, the glutathione system. Hypoxic preconditioning increased the level of PGC-1α expression in the right ventricle, led to the activation of energy metabolism, increased mitochondrial dynamics with the elimination of damaged organelles by mitophagy and biogenesis of new mitochondria against the background of a decrease in mitochondrial dysfunction. After ischemia-reperfusion in the myocardium of insulin-resistant rats, limitations in mitochondrial damage and manifestations of their dysfunction were observed. Preconditioning contributed to a decrease in infarct size, enhanced the mitoprotective effect in the ischemic heart. Insulin resistance contributed to the intensification of PGC-1α-dependent mitochondrial mechanisms of protection against ischemic damage in the myocardium. Hypoxic preconditioning enhanced the myoprotective effect in insulin-resistant hearts compared with intact myocardium, leading to a reduction in myocardial infarct size during isolated heart ischemia-reperfusion, but the antioxidant effect was partially lost.