Purpose Recent studies showed that women after surgery are at higher risk of delivering small-for-gestational infants. Thus, this study aims to investigate longitudinal changes of fetal subcutaneous adipose tissue thickness (FSCTT) of fetuses conceived after gastric bypass surgery as compared to BMI-matched controls. Methods Retrospective cohort study measuring ultrasound-derived longitudinal trajectories of abdominal FSCTT in 41 singleton pregnancies after gastric bypass surgery compared to 41 BMI-matched controls and 64 obese mothers.Results FSCTT was significantly lower in fetuses of women after GB as compared to BMI-matched controls in the second (mean difference 1.38 mm, p < 0.001) and third trimester of gestation (mean difference 3.37 mm, p < 0.001). Longitudinal analysis revealed significant differences in mean FSCTT trajectories between offspring's in GB mothers, BMI-matched, or obese controls. The ratio of FSCTT and abdominal circumference remained constant in the BMI-matched control group whereas it significantly decreased in fetuses of women after GB. Despite remarkable differences were observed in longitudinally assessed FSCTT, further analyses in the GB subgroup revealed that FSCTT were not influenced by OGTT mean or 120 min glucose values, biochemically hypoglycemia, time since bariatric surgery, or weight loss since surgery. Conclusion In fetuses of mothers with history of bariatric surgery, abdominal FSCTT was markedly reduced. While the underlying mechanisms are not fully understood, a multifactorial genesis including nutritional deficiencies and altered metabolism after bariatric surgery is assumed.