The present study investigated the association between protein intake and lean mass according to obesity status over a 12-year period. Data on 4412 participants aged 40–69 years were obtained from the Korean Genome and Epidemiology Study. The usual dietary protein intake of these participants was assessed at baseline using a semi-quantitative FFQ. Body composition was measured using bioelectrical impedance analysis at baseline and after a 12-year follow-up. Linear mixed-effects models were used to examine the associations between lean mass after a 12-year follow-up and protein intake at baseline. After adjusting for covariates and lean mass at baseline, comparisons between the highest and lowest tertiles revealed that dietary protein intake was positively associated with lean mass in both men (β = 0·79, P = 0·001) and women (β = 0·28, P = 0·082) after the 12-year period; however, those differences were attenuated after additional adjustment for fat mass at baseline and were stronger in the normal-weight group (men, β = 0·85, P = 0·002; women, β = 0·97, P < 0·001) but were not detected in the obese group. In the obese group, age (men, β = 4·08, P < 0·001; women, β = 2·61, P < 0·001) and regular physical activity (men, β = 0·88, P = 0·054; women, β = 0·76, P < 0·001) were significantly associated with lean mass after 12 years of follow-up. The results of the present study showed that protein intake may contribute to the prevention of ageing-related lean mass loss; however, the impact of this intake may vary depending on obesity status. Therefore, the maintenance of a healthy body weight during ageing through enhanced protein intake is likely to confer health benefits.