Aims Differences in fibre‐type composition of skeletal muscle have been associated with obesity and insulin resistance. As a poor nutrient environment early in life is a predisposing factor for the development of obesity and related metabolic diseases at adulthood, this study aimed at determining the long‐term consequences of maternal undernutrition on the structural and metabolic properties of two skeletal muscles characterized by their different fibre‐type composition and metabolic properties. Methods The fibre‐type composition and enzymatic activities of hexokinase (HK), beta‐hydroxyacyl‐CoA dehydrogenase (β‐HAD) and citrate synthase (CS) were measured in soleus and extensor digitorum longus (EDL) muscles from adult rats born to dams fed a control (17% protein) or a low‐protein [8% protein (PR)] diet throughout pregnancy and lactation. In addition, the expression levels of several genes regulating glycolysis, fatty acid oxidation and mitochondrial biogenesis were determined by real‐time PCR. Results Protein rats exhibited enhanced density of type II fibres along with decreased rate of fatty acid oxidation and glycolysis in soleus but not EDL. Malnourished rats exhibited also a different gene expression profile in soleus and EDL. Altogether, these alterations correspond to a state of energy deficiency and are present in animals which do not show yet any sign of obesity or glucose intolerance. Conclusion We conclude that maternal protein restriction alters in the long term the structural and enzymatic properties of offspring skeletal muscle in a fibre‐type‐dependent manner. These alterations might have a causative role in the development of obesity and related metabolic disorders later in life.