Large-eddy simulation is used to study the influence of free-atmosphere stratification on the structure of atmospheric boundary-layer flow inside and above very large wind farms, as well as the power extracted by the wind turbines. In the simulations, tuning-free Lagrangian scale-dependent dynamic models are used to model the subgrid-scale turbulent fluxes, while the turbine-induced forces are parameterized with an actuator-disk model. It is shown that for a given surface cover (with and without turbines) thermal stratification of the free atmosphere reduces the entrainment from the flow above compared with the unstratified case, leading to lower boundary-layer depth. Due to the fact that in very large wind farms vertical energy transport associated with turbulence is the only source of kinetic energy, lower entrainment leads to lower power production by the wind turbines. In particular, for the wind-turbine arrangements considered in the present work, the power output from the wind farms is reduced by about 35% when the potential temperature lapse rate in the free atmosphere increases from 1 to 10 K/km (within the range of values typically observed in the atmosphere). Moreover, it is shown that the presence of the turbines has significant effect on the growth of the boundary layer. Inspired by the obtained results, a simple one-dimensional model is developed to account for the effect of free-atmosphere stability on the mean flow and the power output from very large wind farms.