Objectives: Obesity is a major health concern worldwide and it reportedly associated with chronic kidney disease (CKD). Although body mass index (BMI) is a common measure of obesity, there are several concerns regarding its accuracy and ability to measure fat content, muscle mass, and overall body composition. This study aimed to evaluate the risk of CKD development in a middle-aged population in association with various body composition metrics. Methods: From a prospective cohort of 10030 middle-aged adults, we enrolled 6727 for whom baseline and follow-up data were available. We collected data pertaining to participants' BMI, manually measured waist–hip ratio (WHR), and various measurements of bioelectrical impedance analysis (BIA), including total body fat content, muscle content, and calculated WHR, and classified the participants into quintiles accordingly. CKD was defined as an estimated glomerular filtration rate (eGFR) <60 ml/min/1.73 m2 in follow-up laboratory tests.  Results: While an increase in BMI, WHR, and total body fat were associated with an elevated risk of CKD, an increase in total body muscle decreased the risk. Among the body composition metrics, WHR measured by BIA had the highest predictive value for CKD (C-statistics: 0.615). In addition, participants who were “healthy overweight, (defined as low WHR but high BMI), exhibited a 62% lower risk of developing CKD compared to those with “normal-weight obesity,” (defined as high WHR despite a normal BMI). Conclusions: We suggest that central obesity measured by BIA is a more accurate indicator than BMI for predicting the development of CKD.