Background Individuals in isolated conditions and extreme environments can experience debilitating side effects from their environment, which may include a significant decrease in fat-free mass (FFM) from disuse and inadequate nutrition. At its most severe, the decrease in FFM may lead to sarcopenia and frailty. Although there are dietary and physical activity countermeasures, there lacks accessible methods to quantify regional and total FFM during long-isolated missions. The objective of this study was to determine the strengths and weaknesses of three-dimensional optical (3DO) imaging for monitoring body shape and composition in either simulated or actual remote and isolated environments.Methods Thirty healthy adults (ASTRO, male = 15) and twenty-two Antarctic Expeditioners (ABCS, male = 18) were assessed for body composition using a whole-body 3DO scanner. The 3D mesh was used as the 3DO scanner’s output. ASTRO participants completed duplicate whole-body 3DO scans while standing and inverted by gravity boots plus a single dual-energy X-ray absorptiometry (DXA) scan. The inverted scans were used as an analog for fluid redistribution from gravity changes. 3DO body composition estimates were compared to DXA with linear regression and reported with the coefficient of determination (R2) and root mean square error (RMSE). Duplicate 3DO scans were used for test-retest precision, which was reported with the percent coefficient of variation (%CV) and RMSE. ABCS participants received only duplicate whole-body 3DO scans on a monthly basis. An existing body composition model was used to estimate fat mass (FM) and FFM composition and longitudinal change from 3DO meshes.Results Standing ASTRO 3DO meshes achieved an R2 of 0.76, 0.97, and 0.78 with an RMSE of 2.62 kg, 2.04 kg, and 0.06 kg for FM, FFM, and visceral adipose tissue (VAT), respectively, in comparison to DXA. Inverted 3DO meshes achieved an R2 of 0.52, 0.93, and 0.39 with an RMSE of 2.84 kg, 3.23 kg, and 0.11 kg for FM, FFM, and visceral adipose tissue (VAT), respectively, in comparison to DXA. Test-retest precision of inverted 3DO meshes had good precision in total fat-free as well as arm, leg, and trunk fat-free mass (%CV = 2.3%, 2.95%, 1.34%, and 1.55%; RMSE = 1.32, 0.12, 0.14, and 0.47 kg, respectively). For the ABCS arm, mean weight, FM, and FFM changes were − 0.47 kg, 0.06 kg, and − 0.54 kg, respectively.Conclusion Simulated weightlessness and fluid redistribution decreased the accuracy of estimated body composition values from 3DO scans. However, FFM was the most robust. Overall, 3DO imaging showed good absolute accuracy and precision for body composition assessment in isolated conditions and remote environments.