Summary Calorie restriction (CR) reduces bone quantity but not bone quality in rodents. Nothing is known regarding the long‐term effects of CR with adequate intake of vitamin and minerals on bone quantity and quality in middle‐aged lean individuals. In this study, we evaluated body composition, bone mineral density (BMD), and serum markers of bone turnover and inflammation in 32 volunteers who had been eating a CR diet (∼35% less calories than controls) for an average of 6.8 ± 5.2 years (mean age 52.7 ± 10.3 years) and 32 age‐ and sex‐matched sedentary controls eating Western diets (WD). In a subgroup of 10 CR and 10 WD volunteers, we also measured trabecular bone (TB) microarchitecture of the distal radius using high‐resolution magnetic resonance imaging. We found that the CR volunteers had significantly lower body mass index than the WD volunteers (18.9 ± 1.2 vs. 26.5 ± 2.2 kg m −2 ; P = 0.0001). BMD of the lumbar spine (0.870 ± 0.11 vs. 1.138 ± 0.12 g cm −2 , P = 0.0001) and hip (0.806 ± 0.12 vs. 1.047 ± 0.12 g cm −2 , P = 0.0001) was also lower in the CR than in the WD group. Serum C‐terminal telopeptide and bone‐specific alkaline phosphatase concentration were similar between groups, while serum C‐reactive protein (0.19 ± 0.26 vs. 1.46 ± 1.56 mg L −1 , P = 0.0001) was lower in the CR group. Trabecular bone microarchitecture parameters such as the erosion index (0.916 ± 0.087 vs. 0.877 ± 0.088; P = 0.739) and surface‐to‐curve ratio (10.3 ± 1.4 vs. 12.1 ± 2.1, P = 0.440) were not significantly different between groups. These findings suggest that markedly reduced BMD is not associated with significantly reduced bone quality in middle‐aged men and women practicing long‐term calorie restriction with adequate nutrition.