Previously we have reported an association between maternal vitamin D and offspring bone as measured by dual-energy X-ray absorptiometry. It is plausible that shared genetics might confound associations between maternal vitamin D in pregnancy and offspring bone measures. We aimed to determine whether such associations are independent of maternal bone quality. Data for this analysis were derived from 168 mother–child pairs who returned at the 11-year follow-up of the vitamin D in pregnancy study. Gestational 25-hydroxyvitamin D [25(OH)D] was assessed by radioimmunoassay in early pregnancy at recruitment (before 16 weeks gestation) and later in pregnancy (28–32 weeks gestation). Bone quality was assessed for mothers and children at the calcaneus using quantitative ultrasound (Achilles InSight, GE). Speed of Sound (SOS), Broadband Ultrasound Attenuation (BUA) and Stiffness Index (SI) were the outcomes of interest. Maternal 25(OH)D in early pregnancy was associated with offspring SOS (β 1.46 m/s 95% CI 0.12, 2.8). When separated by sex, there was no association between maternal 25(OH)D at recruitment and offspring SI (r = − 0.05, p = 0.68), SOS (r = 0.11, p = 0.34) or BUA (− 0.09, p = 0.43) in girls. In boys, maternal 25(OH)D at recruitment was associated with SI (r = 0.21, p = 0.048), and SOS (r = 0.24, p = 0.03) but not BUA (r = 0.10, p = 0.37). Adjustment for the offspring factors and respective maternal QUS parameter did not attenuate associations between maternal 25(OH)D in early pregnancy with offspring SOS, nor SI. There was no association with BUA. Furthermore, there was no association between maternal 25(OH)D in late pregnancy with any offspring QUS parameter. These prospective data support existing evidence of a positive relationship between maternal 25(OH)D levels during early pregnancy and measures of bone health of offspring in childhood, independent of maternal bone phenotype.