Background Chronic kidney disease (CKD) is a non-communicable disease; it is a major cause of morbidity and mortality in Nigeria as the incidence has been increasing in Nigeria over the last few years. A low-protein diet supplemented with ketoacids has been duly documented to reduce the malnutrition associated with CKD as well as improve estimated glomeruli filtration rate while delaying the onset of dialysis in predialysis CKD patients. Objective The aim of this study was to determine the effects of a low-protein diet supplemented with ketoacids compared to a conventional low protein on nutritional indices in predialysis CKD patients. Methods and materials A randomized controlled trial with a total of 60 participants was conducted at Delta State University Teaching Hospital (DELSUTH), Oghara, Nigeria. Participants were patients older than 18 years with CKD stage 3-5 who were not on dialysis. They were recruited and randomized into the intervention group (low-protein diet supplemented with ketoacids) with 30 participants and the non-intervention group (low protein with placebo) with 30 participants. The mean outcome was changed in the nutritional indices from baseline till the end of the study. Results A total of 60 patients were randomly allocated to receive a low-protein diet supplemented with ketoacids (n=30) or control (n=30). All participants were included in the analysis of all outcomes. The mean change score in serum total protein, albumin, and triglycerides between the intervention and non-intervention groups were 1.1±1.1 g/dL vs 0.1±1.1 g/dL (p<0.001), 0.2±0.9 g/dL vs -0.3±0.8 g/dL (p<0.001), and 3.0±3.5 g/dL vs 1.8±3.7 g/dL, respectively. Conclusion and recommendation The use of low-protein diet supplemented with ketoacids improved the anthropometric and nutritional indices in patients with stage 3-5 CKD.