A growing concern is associated to the greenhouse gases emissions of superyachts, consequently alternative fuels are introduced to the market. For the yachting decarbonisation, this work focuses on hydrotreated vegetable oil (HVO) and methanol. Nevertheless, the uncertain global availability of these fuels can undermine the operations of ocean-crossing superyachts. Thus, a multi-fuel system is installed allowing for fuels switchover and built-in flexibility. Moreover, non-dedicated tanks are installed for the alternative storage of HVO and methanol to make optimal use of the tanks’ capacity. However, the alternative storage of HVO and methanol causes mutual fuels’ contamination. The lack of standards and research on accepted fuels impurity makes full fuels’ separation relevant to be explored. In this work, to avoid degradation of dual-fuel engines or fuel cells, gravity-settling tanks and disc-bowl centrifuges were studied to separate HVO-methanol mixtures. Shake tests were conducted on HVO-methanol mixtures to quantify the separation time and relative concentrations to obtain complete gravity separation. The gravity tests revealed methanol traces in HVO for all the tested mixtures within the 1 hour-3 days observation time, due to the low-density difference between the fuels. This makes the use of gravity-settling tanks impractical onboard for quasi-instantaneous fuels supply to the converters. A mathematical model was developed for disc-bowl centrifuges to assess the separator performance and separation time. Furthermore, the centrifuge was sized by providing the separator working conditions for varying engine modes. Moreover, spin tests were conducted to validate the mathematical model. The model showed that full separation is achievable with a larger centrifuge compared to existing designs. The larger design is due to the low-density difference between the fuels. The maximum separation time ranges from 5-10 minutes. Nevertheless, all the tested mixtures with the spin tests failed at achieving a state of full separation due to the dilution of a certain residual volume in the continuous liquid. The discrepancy between the mathematical model and the spin test results can lie in the neglected diluted phase of the dispersed fuel in the continuous liquid in the mathematical model. However, the mathematical model is a good tool to simulate the dynamic behaviour of the dispersed droplets. Consequently, the onboard use of a centrifuge for separating HVO-methanol mixtures should be evaluated by quantifying the concentration of the fuels’ mixture entering the separator tailored per yacht. Furthermore, tests on dual-fuel engines or fuel cells are recommended to establish tolerable limits of fuel’s contamination.