Genetically identical cloned pigs should in principle eliminate biological variation and provide more pronounced effects when subjected to, e.g., dietary interventions, but little is known about how phenotype and phenotypic variation is affected by cloning. Therefore, an investigation of the metabolome of cloned pigs compared to normal control pigs was performed to elucidate the variation and possible differences in the metabolic phenotypes during a dietary intervention. A total of 19 control pigs and 17 cloned pigs were given the same high-energy dense diet either ad libitum or in a restricted manner (60% of ad libitum) for ∼6 months, and plasma was subjected to liquid chromatography-mass spectrometry nontargeted metabolomics and biochemical analyses. Low systemic levels of IGF-1 could indicate altered growth conditions and energy metabolism in cloned pigs. In response to ad libitum feeding, clones had a decreased energy intake and lower weight gain compared to controls, and plasma lipid profiles were changed accordingly. Elevated lactate and decreased creatine levels implied an increased anaerobic metabolism in ad libitum fed clones. Less interindividual variation between cloned pigs was however not established, suggesting a strong role for epigenetics and/or the gut microbiota to develop variation.