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Background and objectives: Diabetes is largely prevalent in the chronic kidney disease (CKD) population. Both conditions have metabolic and nutritional abnormalities that affect body composition and the presence of diabetes makes the dietary management of CKD patients more difficult. The aim of this study was to assess peculiar nutritional and functional aspects of diabetic patients in an adult/elderly CKD population, and their predictive significance. Materials and methods: This prospective cohort study included 144 out-patients aged >55 years, affected by stage 3b-4 CKD, on tertiary care clinic; 48 (40 males) were type 2 diabetics and 96 (80 males) were nondiabetics. The two groups have similar age, gender, and residual renal function (30 ± 9 vs. 31 ± 11 mL/min×1.73). All patients underwent a comprehensive nutritional and functional assessment and were followed for 31 ± 14 months. Results: Diabetic CKD patients showed higher waist circumference and fat body mass, lower muscle mass, and lower number of steps per day and average daily METs. Meanwhile, resting energy expenditure (REE), as assessed by indirect calorimetry, and dietary energy intake were similar as well as hand-grip and 6 min walking test. Diabetic patients did not show a greater risk for all-cause mortality and renal death with respect to nondiabetics. Middle arm muscle circumference, phase angle, serum cholesterol, and serum albumin were negatively related to the risk of mortality and renal death after adjustment for eGFR. Conclusions: CKD diabetic patients differed from nondiabetics for a greater fat mass, lower muscle mass, and lower physical activity levels. This occurred at the same REE and dietary energy intake. The outcome of diabetic or nondiabetic CKD patients on tertiary care management was similar in terms of risk for mortality or renal death. Given the same residual renal function, low levels of muscle mass, phase angle, serum albumin, and cholesterol were predictive of poor outcome. Overall, a malnutrition phenotype represents a major predictor of poor outcome in diabetic and nondiabetic CKD patients.