Shallow bottom boundary conditions (BBCs) in the soil components of general circulation models (GCMs) impose artificial limits on subsurface heat storage. To assess this problem we estimate the subsurface heat content from two future climate simulations and compare to that obtained from an offline soil model (FDLSM) driven by GCM skin temperatures. FDLSM is then used as an offline substitute for the subsurface of the GCM ECHO-G. With a 600-m BBC and driven by ECHO-G future temperatures, the FDLSM subsurface absorbs 6.2 (7.5) times more heat than the ECHO-G soil model (10 m deep) under the Intergovernmental Panel on Climate Change (IPCC) A2 (B2) emission scenario. This suggests that shallow BBCs in GCM simulations may underestimate the heat stored in the subsurface, particularly for northern high latitudes. This effect could be relevant in assessing the energy balance and climate change in the next century.