The Strategic Transport Research and Innovation Agenda (STRIA) roadmap on low-emission alternative energy for transport was updated in 2020. This report provides a comprehensive analysis of research and innovation in low-emission alternative energy for transport in selected European Union (EU) funded ongoing projects with end dates from 2019 onwards. It considers the latest developments in the field and includes hydrogen, which is covered in the scope of the updated roadmap on low-emission alternative energy for transport. It identifies relevant researched technologies by fuel type and their phase of development. Results show that Liquefied Natural Gas (LNG) refuelling stations followed by biofuels for road transport and alternative aviation fuels are among the researched technologies with the highest investments. Moreover, hydrogen receives the largest share, with 67 projects and the total project value exceeding €1.2 bn. Methane based fuels (e.g. Compressed Natural Gas (CNG), LNG) receive the second greatest attention concerning the number of projects (60) and the level of funding (€944 m), whilst there are only seven research projects still ongoing relating to Liquefied Petroleum Gas (LPG). Alcohols, esters and ethers (31 projects and €241 m) and Synthetic Paraffinic and Aromatic fuels (SPF) (35 projects and €305 m) are in between. So far, road transport has the highest use of alternative fuels in the transport sector. Despite the financial support from the EU, advances have yet to materialise, suggesting that EU transport decarbonisation policies should not consider a radical or sudden change, and therefore, transition periods are critical. It is also noteworthy that there is no silver bullet solution to decarbonisation and the proper use of the various alternative fuels available will be crucial.