The global obesity epidemic is a major public health concern, and accurate diagnosis is essential for identifying at-risk individuals. Three-dimensional (3D) body scanning technology offers several advantages over the standard practice of tape measurements for diagnosing obesity. This study was conducted to validate body scan data from a German population-based cohort and explore clinical implications of this technology in the context of metabolic syndrome. We performed a cross-sectional analysis of 354 participants from the Study of Health in Pomerania that completed a 3D body scanning examination. The agreement of anthropometric data obtained from 3D body scanning with manual tape measurements was analyzed using correlation analysis and Bland-Altman plots. Classification agreement regarding abdominal obesity based on IDF guidelines was assessed using Cohen's kappa. The association of body scan measures with metabolic syndrome components was explored using correlation analysis. Three-dimensional body scanning showed excellent validity with slightly larger values that presumably reflect the true circumferences more accurately. Metabolic syndrome was highly prevalent in the sample (31%) and showed strong associations with central obesity. Using body scan vs. tape measurements of waist circumference for classification resulted in a 16% relative increase in the prevalence of abdominal obesity (61.3% vs. 52.8%). These results suggest that the prevalence of obesity may be underestimated using the standard method of tape measurements, highlighting the need for more accurate approaches.