Abstract Background Prenatal treatment with dexamethasone (DEX) reduces virilization in girls with congenital adrenal hyperplasia (CAH). The treatment is effective but may result in long-lasting adverse effects. In this study we explore the effects of DEX on metabolism in individuals not having CAH but treated with DEX during the first trimester of fetal life. Method All DEX-treated participants (n = 40, age range 5.1-26.4 years) and controls (n = 75, age range 4.5-26.6 years) were assessed with fasting blood samples to measure blood count, renal function, glucose homeostasis, and serum lipid profiles. Results There were no significant differences between DEX and control participants for birth parameters, weight and height, or body mass index at the time of testing. Analyzing the entire cohort, we found no significant effects of DEX on blood count, renal function, or serum lipid profiles. However, a lower HOMA-β index in the DEX-treated individuals (U = 893.0; P = 0.049) was observed. Post hoc analyses revealed an effect in girls (U = 152.5; P = 0.024) but not in boys (U = 299.5; P = 0.550). The effect on HOMA-β persisted (U = 117.5; P = 0.048) after analyzing data separately in the participants < 16 years of age. In addition, we observed higher plasma glucose levels (F = 14.6; P = 0.001) in the DEX-treated group. The participants ≥ 16 years of age in the DEX-treated group had significantly higher total plasma cholesterol (F = 9.8; P = 0.003) and higher low-density lipoprotein cholesterol levels (F = 7.4; P = 0,009). Conclusion Prenatal DEX exposure in early pregnancy has negative effects on beta-cell function and lipid profile in individuals without CAH already at a young age.