In the yachting decarbonisation by 2030, multiple fuels usage provides flexibility to ocean-crossing superyachts in a scenario where alternative fuels become progressively available worldwide. Hydrotreated vegetable oil (HVO) and methanol (MeOH) are selected among all sustainable fuels. The desired flexibility can be achieved with a multi-fuel system. To make optimal use of the tanks' capacity, HVO and methanol are alternately stored in all tanks, yielding mutual fuels’ contamination. The lack of standards and research on accepted fuels impurity makes full fuels separation relevant to be explored to avoid performance degradation of dual-fuel engines. Identified technologies for separating HVO-methanol mixtures are gravity-settling tanks and disc-bowl centrifuges. Shake tests were conducted on HVO-MeOH mixtures to quantify the separation time and relative concentrations to obtain complete gravity separation. The fuels were poured into a beaker with methanol at 1, 5, 10-70% v/v. Visual and microscopic examinations identified MeOH traces in HVO. The tests revealed that full separation was not achieved in the 1 hour-3 days observation time, due to the low-density difference between the fuels. Hence, as the experimental outcomes evidenced incomplete HVO-methanol separation, centrifuges were studied to achieve this goal. A mathematical model was developed for disc-bowl centrifuges to assess the separator performance and separation time. Integration with a multi-fuel system helped size the centrifuge by providing the separator working conditions for varying engine modes. Complete separation is theoretically possible with a separator larger than the existing disc-bowl designs, due to the low-density difference between methanol and HVO. The maximum separation time ranges 5-10 minutes for MeOH droplets ranging 12-16 µm in diameter. Droplets with a diameter outside this range coalesce quasi-instantaneously. Lastly, when integrating the centrifuge within the multi-fuel system, HVO and MeOH buffer tanks are needed onboard, respectively with about 1/3 and 1/20 of the storage tanks' capacity.