Gallium 68 (68Ga)-labeled DOTA-conjugate ibandronic acid (DOTA-IBA) has been successfully synthesized and utilized for bone metastasis imaging. This study compares the diagnostic efficacy between 68Ga-DOTA-IBA and fluorine 18 (18F)-labeled fluorodeoxyglucose (FDG) in detecting bone metastases. This prospective study, conducted from October 2022 to September 2023, analyzed images from participants who underwent 68Ga-DOTA-IBA PET/CT and 18F-FDG PET/CT scans. Lesions were classified into five groups based on anatomical location (limbs, vertebrae, pelvis, ribs, and skull). Morphological bone changes were categorized as osteolytic, osteoblastic, or mixed. The semi-quantified radiotracer uptake, measured by the maximum standardized uptake value (SUVmax), was compared using a paired t-test. Detection rates between the two scans were analyzed using the McNemar test. A total of 46 participants (median age: 64 years [interquartile range: 53-68 years], 28 men) were evaluated. 68Ga-DOTA-IBA demonstrated higher diagnostic efficacy than 18F-FDG in detecting bone metastases in the limbs (73.2% vs. 64.1%), vertebras (78.1% vs. 67.4%), ribs (86.6% vs. 62.2%), pelvis (78.6% vs. 68.9%), and skulls (80.0% vs. 38%). For osteoblastic lesions, the detection rate for 68Ga-DOTA-IBA and 18F-FDG was 83.3% and 51.5% respectively (P < 0.001). The SUVmax of 68Ga-DOTA-IBA was 7.88 (95% CI 7.09-8.66), which was higher than that of 18F-FDG at 3.96 (95% CI 3.57-4.35) (P < 0.001). In participants with prostate cancer, the detection rate of 68Ga-DOTA-IBA and 18F-FDG was 84.7% and 55.0% respectively (P < 0.001). The SUVmax of 68Ga-DOTA-IBA was 10.44 (95% CI 8.57-12.30), which was higher than that of 18F-FDG 4.29 (95% CI 3.51-5.07) (P < 0.001). 68Ga-DOTA-IBA PET/CT demonstrates superior diagnostic performance over 18F-FDG PET/CT in detecting bone metastases, particularly in osteoblastic lesions and prostate cancer cases.© 2025. The Author(s).