Objective <p>This study aimed to assess the accuracy of fat fraction estimation with clinically available Dixon sequences in normal-appearing marrow and bone metastases in the pelvis of metastatic prostate cancer patients.</p> Methods <p>A prospective single-centre study was conducted with metastatic prostate cancer patients and healthy volunteers. Linearity and bias of fat fraction estimates from clinically available Dixon sequences were assessed against a 6-point PDw gradient echo (q-Dixon) sequence measuring the reference standard proton density fat fraction. Lesion fat fraction estimates were cross-compared using the Friedman test. Repeatability in volunteers was evaluated with Bland-Altman plots. Sensitivity of fat fraction estimates using TSE-Dixon sequences to specific absorption rate (SAR) related modifications were evaluated with correlation plots.</p> Results <p>Thirty-three patients were recruited for this study. Significant (<i>p</i> &lt; 0.05) absolute bias (12.4%) was demonstrated in the T1-weighted (T1w) Dixon measurements against the q-Dixon. Significant differences (<i>p</i> &lt; 0.05) between fat fraction estimates provided by the T1w Dixon and PDw Dixon sequences were observed in 13 active and 6 treated lesions. Repeatability coefficients for fat fraction estimates ranged from 5.9 to 9.0% in the pelvic tissues of healthy volunteers. Reduction of slice number with repetition time for SAR had the greatest effect, reaching a maximum difference in fat fraction of 14.7% from the q-Dixon for the T2w-TSE Dixon in bone marrow.</p> Conclusions <p>T1w Dixon methods can detect post-treatment changes but remain confounded by relaxation time biases. While all Dixon methods showed good repeatability, careful choice of SAR-related modifications is critical to maintaining accuracy for PD- and T2-weighted TSE sequences.</p> Key Points <p><Emphasis Type="BoldItalic">Question</Emphasis> <i>The clinical validity of signal-weighted fat fraction estimates versus proton density fat fraction for characterising metastatic bone lesions has not been fully assessed.</i></p> <p><Emphasis Type="BoldItalic">Findings</Emphasis> <i>T1-weighted Dixon sequences in line with whole-body MRI international guidelines demonstrate significant fat fraction bias, particularly in lesions and muscle.</i></p> <p><Emphasis Type="BoldItalic">Clinical relevance</Emphasis> <i>Fat fraction estimation using T1-weighted Dixon sequences recommended in international guidelines are highly sensitive to relaxation time biases, making underlying physiological changes potentially ambiguous.</i></p> Graphical Abstract <p></p>