Abstract The war in Ukraine caused Europe to more than double its imports of liquefied natural gas (LNG) in only one year. In addition, imported LNG remains a crucial source of energy for resource-poor countries, such as Japan, where LNG imports satisfy about a quarter of the country’s primary energy demand. However, an increasing number of countries are formulating stringent decarbonization plans. Liquefied hydrogen and liquefied ammonia coupled with carbon capture and storage (LH2-CCS, LNH3-CCS) are emerging as the front runners in the search for low-carbon alternatives to LNG. Yet, little is currently known about the full environmental profile of LH2-CCS and LNH3-CCS because several characteristics of the two alternatives have only been analyzed in isolation in previous work. Here we show that the potential of these fuels to reduce greenhouse gas (GHG) emissions throughout the supply chain is highly uncertain. Our best estimate is that LH2-CCS and LNH3-CCS can reduce GHG emissions by 25%–61% relative to LNG assuming a 100 year global warming potential. However, directly coupling LNG with CCS would lead to substantial GHG reductions on the order of 74%. Further, under certain conditions, emissions from LH2-CCS and LNH3-CCS could exceed those of LNG, by up to 44%. These results question the suitability of LH2-CCS and LNH3-CCS for stringent decarbonization purposes.