Skeletal muscle atrophy is a clinically important outcome of disuse due to injury, immobilization and bed rest. Disuse atrophy is accompanied by mitochondrial dysfunction which likely contributes to activation of the muscle atrophy program. However, the linkage of muscle mass and mitochondrial energetics, during disuse atrophy and its recovery is incompletely understood. Transcriptomic analysis of muscle biopsies from healthy older adults subject to complete bed rest revealed marked inhibition of mitochondrial energy metabolic pathways. To determine the temporal sequence of muscle atrophy, and changes in intramyocellular lipid and mitochondrial energetics, we conducted a time course of hind limb unloading induced atrophy in adult mice. Mitochondrial respiration and calcium retention capacity were diminished while HOemission was increased in as soon as 3 days of unloading, prior to significant muscle atrophy. These changes were associated with a decrease in total cardiolipin and profound changes in remodeled cardiolipin species. Hindlimb unloading performed in muscle-specific PGC-1a/bknockout mice, a model of mitochondrial dysfunction, did not affect muscle atrophy but impacted muscle function. These data suggest early mitochondrial remodeling affects muscle function but not mass during disuse atrophy. Early alterations in mitochondrial energetics and lipid remodeling may represent novel targets to prevent muscle functional impairment caused by disuse and to enhance recovery from periods of muscle atrophy.