Background During the past few decades, overweight and obesity have become a global health hazard. The estimation and documentation of obesity are important in countries like India that have a broad diversity of populations. However, there is discrepancy in the various adiposity indicators used to estimate obesity. The present study examines population-specific associations between percent body fat (%BF) and adiposity variables among females in three population groups. Materials and methods A cross-sectional study was conducted among Jat, Mizo, and Liangmai communities of India. Data were collected using interview schedules and somatometric measurements based on ISAK protocols. Body density was calculated from skinfold measurements and the Siri equation was used to determine %BF. WHO cut-offs were used for waist circumference (WC), waist-to-hip ratio (WHR), and body mass index (BMI), whereas Ashwell and Gibson and American Council for Exercise cut-offs were used for waist-to-height ratio (WHtR) and %BF, respectively. Results Obesity variables are differentially distributed across the three populations. The mean values of %BF and WHtR were the highest among the Liangmai, whereas BMI, WC, and WHR were the highest among the Mizo. Conclusion All of the selected adiposity indicators (WC, WHR, WHtR, and BMI) in all three populations were significantly positively correlated with %BF. Thus, %BF should be incorporated with other adiposity indicators as well, for a better understanding and categorisation of obesity among different populations.