The transformation towards a climate neutral Swedish society means a rapid progress towards electrification and new types of fuels. The Swedish Armed Forces is tasked to reduce its dependence on fossil fuels but this pose challenges as the operational requirements on fuels in the Armed Forces are high and many vehicle systems have very long life-times (+30 years). This study analyse some of the Armed Forces challenges to transform in line with the civil developments toward electrification and fossil free fuels. Given the current doctrine´s dependence on mobility, it is unlikely that electrification will find any significant use in the Armed Forces in the short-term. However, the Armed Forces is influenced by the civilian development toward electrification and the large uncertainty on technology choices that will dominate air, sea and heavy long range land based transports. The recommendation is to intensify the work on certifying the Air Force aircraft systems for bio- or synthetic fuels. Here the potential for carbon dioxide emissions savings are highest and the technical uncertainty is at the same time the lowest. There is also a clear need for more studies on how the civil transformation can affect operational requirements, implications on cost, organization and logistics. An important task for future studies is to assess if liquid fuels synthesized from hydrogen can be the long-term option that the Swedish Total Defence concept need in times of crisis and armed conflict.