Background: Beta-thalassemias are blood disorders characterized by poorly understood clinical phenotypes ranging from asymptomatic to severe anemia. Metabolic composition of the human placenta could be affected by the presence of pathological states such as β-thalassemia. The aim of our study was to describe metabolic changes in chorionic villi samples of fetuses affected by β-thalassemia compared to a control group by applying a metabolomics approach. Methods: Chorionic villi samples were differentiated according to the genetic diagnosis of β-thalassemia: control (Group 1, n = 27); heterozygous (Group 2, n = 7); homozygous (Group 3, n = 7). Gas chromatography−mass spectrometry was used to detect the metabolic composition of the samples. Subsequently, multivariate and univariate statistical analysis was performed. The discriminant metabolites were used to identify the altered pathways. Results: Supervised multivariate models were devised to compare the groups. The model resulting from the comparison between Group 1 and Group 3 was the most significant. Discriminant metabolites were identified, and the most altered pathways were as follows: pentose phosphate pathway (PPP), arachidonic acid metabolism, glycolysis, and gluconeogenesis, suggesting the presence of an energetic shift toward the PPP and the presence of oxidative stress in β-thalassemia chorionic villi samples. Conclusions: The metabolomics approach identified a specific metabolic fingerprint in chorionic villi of fetuses affected by β-thalassemia.