Venous quantitative susceptibility mapping (QSM) enables quantification of venous oxygenation. Flow-compensated acquisition is generally recommended for venous QSM, although its effect on the accuracy of venous susceptibility values has not been systematically evaluated. Moreover, QSM processing methods tend to be optimized for brain parenchyma tissues rather than veins. Here, we compared five different acquisition protocols (incorporating distinct flow compensation schemes) and six QSM processing methods in ten healthy volunteers. We found that venous susceptibility values depend strongly on the QSM pipeline (effect size ηp2=0.861) and much less on acquisition parameters including flow compensation (effect size ηp2=0.016).