Cardiovascular diseases associated with metabolic syndrome remain frequent and still disabling for patients. The uncovering of Ca2+ microdomains between mitochondria and reticulum (SR) in the heart has launched a new area of investigation for cardiometabolic diseases. Here, we sought to determine the structural and functional role of the SR-mitochondria interactions in the mice heart during diabetes. We hypothesized that an alteration of the SR-mitochondria interactions would impair the Ca2+ signaling between the two organelles, thus leading to contractile dysfunction. Mice were either fed with a standard diet (SD: 16.9% proteins, 4.3% lipids) or a high-fat-high-sucrose diet (HFHSD:20% proteins, 36% lipids) for 16 weeks. In the HFHSD group, half of the mice were subjected to metformin gavage, an antidiabetic agent, for the last 4 weeks. Cardiac mitochondria associated membranes (MAM) isolation showed an increased protein amount of MAM/pure mitochondria in the HFHSD group vs. SD mice, which was prevented by metformin treatment (SD: 2.0 ± 0.4, HFHSD: 5.5 ± 0.9, HFHSD + MET: 2.8 ± 0.4, n = 5). After 70 min hypoxia-2 hrs reoxygenation, HFHSD isolated cardiomyocytes displayed higher propidium-iodide positive cells compared to SD and HFHSD + MET groups (60 ± 1 vs. SD: 46 ± 3 and HFHSD + MET: 50 ± 2%, n = 5). Interestingly, histamine-stimulated Ca2+ transfer to mitochondria was reduced by 50% in HFHSD ± MET cardiomyocytes. Concomitantly, IP3R-VDAC interactions assessed by proximity ligation assay were 30–40% reduced in HFHSD ± MET cardiomyocytes. Hence, our data indicate a role for the SR-mitochondria interactions during diabetes in the heart in hypoxia-reoxygenation-induced cell death and in the Ca2+ signaling dysfunction. Indeed, reduced formation of the IP3R-VDAC Ca2+ channeling complex and of the IP3R-stimulated Ca2+ transfer to mitochondria in the HFHSD ± MET cardiomyocytes suggest an inappropriate thickness of the extended MAM (too close or too far) for the IP3R complex formation.