Backgound: Traditional anthropometrics such as body mass index (BMI) or waist circumference (WC) do not fully capture the complex biology of body fat (BF) in the elderly. The Clinica Universidad de Navarra-Body Adiposity Estimator (CUN-BAE) index, based on BMI, is proposed as a better indicator of BF. However, its relation with BMI is not clear. The aim was to compare the agreement between CUN-BAE, BMI, and WC in those aged ≥50 years. Methods: A cross-sectional sample of 3153 Caucasian healthy adults was taken from the MCC-Spain study. The Pearson’s correlation and its 95% confidence interval (CI), adiposity distribution, and Kappa Index (95%CI) were calculated. Results: The correlation of CUN-BAE with WC is 0.18 (95%CI 0.14–0.21) and that with BMI is moderate (r 0.58; 95%CI 0.55–0.60), but both increased strongly by sex. Agreement (normal weight/overweight/obesity) of CUN-BAE with BMI is 7% and with WC is 18%. Conclusions: The correlation and the degree of agreement of CUN-BAE with BMI and WC are low in individuals aged over 50, but it is higher by sex. Thus, this different criterion of obesity may have clinical applications. More studies with a gold standard are needed to evaluate the CUN-BAE in elderly adults.