The dipeptidyl peptidase-4 (DPP-4) inhibitor Linagliptin is known for its role in glucose metabolism and potential cardioprotective effects. This study investigated the cardiac proteome of male and female C57BL/6N mice fed either a normal or high-fat diet, with or without Linagliptin treatment, using a label-free proteomic approach. The analysis revealed significant sex-related metabolic responses, affecting lipid metabolism, oxidative stress, and insulin signaling pathways. Notably, Linagliptin modulated mitochondrial and inflammatory processes, suggesting a potential role in improving cardiac function in obesity. These findings highlight novel biomarkers and molecular mechanisms underlying the cardiometabolic effects of DPP-4 inhibition.