To examine the respective roles of malnutrition and phosphate depletion on muscle exercise capacity and bioenergetics, phosphate‐depleted, either underfed or partly refed rats; phosphate‐supplemented, either underfed or partly refed rats; and well‐nourished control animals were studied, using swim time to exhaustion and31P NMR spectroscopy measurements of muscle phosphocreatine, inorganic phosphate, adenosine triphosphate and intracellular pH. Only partly refed rats displayed hypophosphataemia. Swim time to exhaustion was lower in non‐refed rats than in controls. Among the four groups, both refeeding and phosphate depletion positively affected swim time to exhaustion (both withP<0.02), and swim time to exhaustion was negatively correlated with phosphataemia (P<0.05). At rest, the ratio of muscle phosphocreatine/inorganic phosphate was lower in the phosphate‐supplemented rats than in controls, whereas muscle phosphocreatine/adenosine triphosphate and intracellular pH were comparable. After non‐tetanic stimulation, the muscle phosphocreatine recovery was slower in the four groups than in controls and closely correlated with exhaustion (P<0.01). These findings suggest that malnutrition alters the capacity of muscular work, mainly because of a reduced cell oxidative energy availability. These patterns are improved by partial refeeding and clearly influenced by the level of phosphorus intake, whether depletion is capable of improving metabolic alterations or uncontrolled supplementation is deleterious in malnouris