© 2016, The Author(s). Rapid cuts in greenhouse gas emissions require an almost complete transformation of the energy system to low carbon energy sources. Little consideration has been given to the potential adverse carbon consequences associated with the technology transition. This paper considers the embodied emissions that will occur to replace the UK’s fossil fuel-reliant energy supply with low carbon sources. The analysis generates a number of representative scenarios where emissions embodied in energy systems are integrated within current national climate and energy policy objectives. The embodied emissions associated with a new low carbon energy system are lower than the emissions reduction associated with the low carbon energy sources, confirming that there is a carbon return on investment. However, even if the UK reaches its 2050 territorial climate target, it is estimated that by 2050 an additional 200 Mt CO2 emissions are generated overseas (compared to 128 Mt generated within the UK) in the production of imported fuels and infrastructure components. The cost-optimal model results suggest that more electrification would need to occur, supported by nuclear energy, mainly in replacement of natural gas to mitigate these emissions. However, due to a number of deployment barriers, other policy interventions along the energy supply chain are likely needed, which are discussed alongside the model results. There could be more emphasis on an absolute reduction in energy demand to reduce the scale of change needed in supplying energy; new business models oriented towards performance and not sales; and existing trade schemes and international effort-sharing frameworks could be extended.