Background Maternal nutritional status is an important determinant of intrauterine growth and neonatal size. No published surveys exist on maternal Mediterranean diet intakes and newborn adiposity. The aim of the study was to evaluate the impact of the individual maternal Mediterranean diet on the in-utero body fat formation and cord leptin level in newborns. Pregnant women with a pre-pregnancy body mass index (BMI) between 30 and 35 kg/m2 (n = 118) were assisted for individual dietary counseling based on the Mediterranean diet healthy eating. According to diet adherence, participants (paired mother and newborn) were divided into an intervention group (n = 57) and a control group (n = 61). We examined the association between diet modification and gestational weight gain, maternal, and cord leptin level together with newborn anthropometry (weight and fat mass %). Results Gestational weight gain, newborn birth weight, fat mass %, and cord leptin level lower in the intervention (12.22 ± 1.8 kg, 3.57 ± 0.35 kg, 9.27 ± 2.16 %, 11.78 ± 3.63 ng/ml, p = 000, respectively) than in control group (18.03 ± 3.25 kg, 4.02 ± 0.32 kg, 11.85 ± 2.30 %, 35.37 ± 11.14 ng/ml, respectively. Umbilical cord leptin levels strongly correlated with neonatal fat mass percent in both groups. However, maternal serum leptin did not correlate with the newborn parameters in the intervention group. Conclusion Maternal energy intake from healthy fat and diet intervention is probably associated with decreased fat mass and leptin levels in neonates.