<p>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 (SUV_max), 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 (<i>P</i> &lt; 0.001). The SUV_max 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) (<i>P</i> &lt; 0.001). In participants with prostate cancer, the detection rate of ⁶⁸Ga-DOTA-IBA and ¹⁸F-FDG was 84.7% and 55.0% respectively (<i>P</i> &lt; 0.001). The SUV_max 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) (<i>P</i> &lt; 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.</p>