Objectives: Bioelectrical impedance analysis (BIA) has been recommended for the assessment of body composition in patients with chronic kidney disease (CKD). However, further research investigating the association between segmental BIA parameters and malnutrition in CKD patients, particularly focusing on integration of raw impedance and calculated volumetric data, is warranted. Methods: In this cross-sectional study, 378 patients with CKD stage G3a–4 from the Phase II KoreaN Cohort Study for Outcomes in Patients With CKD, who underwent nutritional assessment from four participating centers, were included. A multi-frequency BIA device was used to assess body composition, including soft lean mass (SLM) at five segments (arms, legs, and trunk). For the analysis of raw impedance data, phase angle (PhA) and impedance measured at 50 kHz were used. Primary outcome was malnutrition, defined as malnutrition inflammation score (MIS) ≥6. Multivariable logistic regression analysis was used to evaluate the association between each BIA parameter and malnutrition risk. Results: Among the study population, 73% were male and 6% had malnutrition. Arm SLM was lower in malnourished patients for both sexes, whereas leg SLM did not show a significant difference. While PhAs in the arm and the leg were lower in malnourished patients, impedance was significantly higher only in the arm. In multivariable logistic regression analysis, lower SLM in the arm was significantly associated with malnutrition risk (adjusted odds ratio [aOR], 0.15 [0.06–0.36]). Furthermore, lower PhA in both the arm (aOR, 0.37 [0.21–0.67]) and the leg (aOR, 0.42 [0.24–0.75]) segments was significantly associated with malnutrition risk, while higher impedance was a significant risk factor only in the arm (aOR, 4.27 [2.26–8.07]). Conclusion: Lower arm SLM, accompanied by lower PhA and higher impedance, is associated with higher malnutrition risk in patients with CKD, suggesting that arm parameters minimize the confounding effects of fluid overload.