Effects of environmental hypoxia on fat-free mass are well studied. Negative energy balance, increased nitrogen excretion, and fat-free mass loss are commonly observed in lowlanders sojourning at high altitude. Reductions in fat-free mass can be minimized if energy consumption matches energy expenditure. However, in nonresearch settings, achieving energy balance during high-altitude sojourns is unlikely, and myofibrillar protein mass is usually lost, but the mechanisms accounting for the loss of muscle mass are not clear. At sea level, negative energy balance reduces basal and blunts postprandial muscle protein synthesis, with no relevant change in muscle protein breakdown. Downregulations in muscle protein synthesis and loss of fat-free mass during energy deficit at sea level are largely overcome by consuming at least twice the recommended dietary allowance for protein. Hypoxia may increase or not affect resting muscle protein synthesis, blunt postexercise muscle protein synthesis, and markedly increase proteolysis independent of energy status. Hypoxia-induced mTORC1 dysregulation and an upregulation in calpain- and ubiquitin proteasome–mediated proteolysis may drive catabolism in lowlanders sojourning at high altitude. However, the combined effects of energy deficit, exercise, and dietary protein manipulations on the regulation of muscle protein turnover have never been studied at high altitude. This article reviews the available literature related to the effects of high altitude on fat-free mass, highlighting contemporary studies that assessed the influence of altitude exposure (or hypoxia) on muscle protein turnover and intramuscular regulation of muscle mass. Knowledge gaps are addressed, and studies to identify effective and feasible countermeasures to hypoxia-induced muscle loss are discussed.