This study aimed to cross-calibrate body composition measures from the GE Lunar Prodigy and GE Lunar iDXA in a cohort of young children. 28 children (mean age 3.4 years) were measured on the iDXA followed by the Prodigy. Prodigy scans were subsequently reanalysed using enCORE v17 enhanced analysis (“Prodigy enhanced”). Body composition parameters were compared across three evaluation methods (Prodigy, Prodigy enhanced, iDXA), and adjustment equations were developed. There were differences in the three evaluation methods for all body composition parameters. Body fat percentage (%BF) from the iDXA was approximately 1.5-fold greater than the Prodigy, whereas bone mineral density (BMD) was approximately 20% lower. Reanalysis of Prodigy scans with enhanced software attenuated these differences (%BF: − 5.2% [95% CI − 3.5, − 6.8]; and BMD: 1.0% [95% CI 0.0, 1.9]), although significant differences remained for all parameters except total body less head (TBLH) total mass and TBLH BMD, and some regional estimates. There were large differences between the Prodigy and iDXA, with these differences related both to scan resolution and software. Reanalysis of Prodigy scans with enhanced analysis resulted in body composition values much closer to those obtained on the iDXA, although differences remained. As manufacturers update models and software, researchers and clinicians need to be aware of the impact this may have on the longitudinal assessment of body composition, as results may not be comparable across devices and software versions.