Muscle uses Ca²⁺ as a messenger to control contraction and relies on ATP to maintain the intracellular Ca²⁺ homeostasis. Mitochondria are the major sub-cellular organelle of ATP production. With a negative inner membrane potential, mitochondria take up Ca²⁺ from their surroundings, a process called mitochondrial Ca²⁺ uptake. Under physiological conditions, Ca²⁺ uptake into mitochondria promotes ATP production. Excessive uptake causes mitochondrial Ca²⁺ overload, which activates downstream adverse responses leading to cell dysfunction. Moreover, mitochondrial Ca²⁺ uptake could shape spatio-temporal patterns of intracellular Ca²⁺ signaling. Malfunction of mitochondrial Ca²⁺ uptake is implicated in muscle degeneration. Unlike non-excitable cells, mitochondria in muscle cells experience dramatic changes of intracellular Ca²⁺ levels. Besides the sudden elevation of Ca²⁺ level induced by action potentials, Ca²⁺ transients in muscle cells can be as short as a few milliseconds during a single twitch or as long as minutes during tetanic contraction, which raises the question whether mitochondrial Ca²⁺ uptake is fast and big enough to shape intracellular Ca²⁺ signaling during excitation-contraction coupling and creates technical challenges for quantification of the dynamic changes of Ca²⁺ inside mitochondria. This review focuses on characterization of mitochondrial Ca²⁺ uptake in skeletal muscle and its role in muscle physiology and diseases.