Limb-girdle muscular dystrophy (LGMD) is a genetic disorder characterized by weakness of predominantly proximal limb and trunk muscles due to progressive muscle tissue degeneration. To date, more than 30 different genetic forms of LGMD have been categorized and several of them are associated with mitochondrial dysfunction. However, the specific and detailed mechanisms that induce mitochondrial dysfunction remain unclear. Here, we pursue a better understanding of how LGMD impacts mitochondria and the involved pathways to guide future therapeutic development. The current study compared early-stage Sgcg-/- mice (a model of LGMDR5) to age and background matched wild-type controls. Tandem mass tagging quantitative proteomic analyses were performed in duplicate to screen a total of 3345 proteins identified from the mouse left ventricle. Among these, we identified 71 proteins with unique peptide and high fidelity score that demonstrated a statistical significance (p-value < 0.05) between LGMD group and the heathy control. STRING interaction network analysis revealed that, in addition to the reduction in many muscle contraction-related proteins, there was a dramatic decrease in the expression of a cluster of proteins involved in ion transport activities, particularly for cation membrane transport. Several of these play a crucial role in mitochondrial function through maintenance of the electrochemical gradient within the mitochondria membrane. This finding is consistent with our isolated cardiac mitochondria assessments that reveled significant decrease in: oxygen consumption (38%), ATP content (53%), and mitochondrial membrane potential (24%). Our study confirms that LGMDR5 impacts cardiac mitochondrial function at the early stages of disease development. Future evaluation of how expression profiles related to mitochondrial function change with disease progression will reveal potential therapeutic targets.