Emissions regulations aimed at reducing carbon dioxide and other emissions are driving commercial research into alternative fuels. Being government owned, naval vessels are exempt from these regulations, but not auxiliary vessels including the RFA and patrol boats. Some governments have committed to meeting regulations where possible and public or even legal pressure may strengthen a requirement for operation on low-or zero emissions fuels in future, even if only in peacetime. These new fuels present major challenges for naval use, such as lower energy density, increased toxicity, increased flammability and explosion risk, which has implications on storage and use. This paper summarises ongoing work using the ZEOLIT tool, previously presented at INEC 2018, to assess the overall ship impacts of adopting alternative fuels over a range of warship sizes, rather than single exemplar designs. Application of methanol and ammonia to a generic frigate design has been found to lead to increases in size that do not seem excessive, and that more efficient but expensive machinery (fuel cells) is desirable as reductions in displacement are significant compared to increases in cost.