Controversy exists on whether animal and plant proteins influence obesity differently. The purpose of this study was to evaluate the association between total, animal, and plant protein intake with the body mass index (BMI), waist circumference (WC), and renal function in the Korean elderly. Study participants included Korean adults aged 60 years or older from the Korean National Health and Nutrition Examination Survey in 2013–2014. Height, weight, and waist circumference were measured and the body mass index was calculated. One-day 24-hour recall data were used to estimate daily total, animal, and plant protein intake. Glomerular filtration rate (GFR) was calculated by using the Modification of Diet in Renal Disease (MDRD) equation. General linear modellings were used to assess the relationships between protein intake, BMI and WC. The mean age was 69.2 ± 0.2 years and 44.2% were male. The total daily protein intake was 1.1 ± 0.02 g/kg/day and 0.9 ± 0.02 g/kg/day for males and females, respectively. Only one third of protein intake was from animal sources. In males, BMI (regression coefficient (95% CI); −1.30 (−1.55, −1.06), p < 0.001; −0.29 (−0.52, −0.05), p = 0.016; −1.30 (−1.8, −1.02), p < 0.001, respectively) and WC (−3.87 (−4.58, −3.16), p < 0.001; −0.90 (−1.58, −0.22), p = 0.010; −3.88 (−4.68, −3.08), p < 0.001, respectively) decreased as daily intake of plant protein (g/kg/day), animal protein (g/kg/day) and total protein (g/kg/day) increased. Similar associations were shown in Korean females. GFR was not associated with protein intake regardless of protein source in both sexes. In Korean adults aged 60 years or older, the protein intake was associated with a favorable obesity index without decrease in renal function. The effect was similar in both males and females, with both animal and plant proteins.