In the present review, we aim to address the current strategies for characterization of the mitochondrial proteome and to summarize the existing knowledge of the proteomic signatures of human skeletal muscle mitochondria in relation to insulin-resistant conditions, such as obesity, T2D, and aging, as well as the effects of exercise, a well-known counteractor of IR. Here, INS is linked to obesity due to melanocortin 4 receptor deficiency.