Variable durations of food restriction (FR) (lasting weeks to years) and variable FR intensities are applied to animals in lifespan-prolonging studies. A reduction in mitochondrial proton leak is suggested as a putative mechanism linking such diet interventions and aging retardation. The early mechanisms of mitochondrial metabolic adaptation induced by FR remain unclear. We investigated the influence of different degrees of FR over three days on mitochondrial proton leak and mitochondrial energy metabolism in rat hind limb skeletal muscle. Animals underwent 25%, 50%, 75% FR and total FR, compared to control rats. Proton leak kinetics and mitochondrial functions were investigated in two mitochondrial subpopulations, intermyofibrillar (IMF) and subsarcolemmal (SSM) mitochondria. Regardless of the degree of restriction, skeletal muscle mass was not affected by 3 days of FR. Mitochondrial basal proton conductance was significantly decreased in 50% restricted rats in both mitochondrial subpopulations (46% and 40% for IMF and SSM respectively), but was unaffected in other groups when compared to controls. State 3 and uncoupled-state 3 respiration rates were decreased in SSM mitochondria, only for 50% restricted rats when pyruvate + malate was used as substrate (-34.5% and -38.9% compared to controls, p < 0.05). IMF mitochondria respiratory rates remained unchanged. Three days of FR, particularly at 50% FR was sufficient to lower mitochondria energetic metabolism in both mitochondrial populations. Our study highlights an early step in mitochondrial adaptation to food restriction and the influence of the severity of restriction on this adaptation. This step may be involved in an aging-retardation process.