- We advance our prior energy- and flux-budget (EFB) turbulence closure model for stably stratified atmospheric flow and extend it to account for an additional vertical flux of momentum and additional productions of turbulent kinetic energy (TKE), turbulent potential energy (TPE) and turbulent flux of potential temperature due to large-scale internal gravity waves (IGW). For the stationary, homogeneous regime, the first version of the EFB model disregarding large-scale IGW yielded universal dependencies of the flux Richardson number, turbulent Prandtl number, energy ratios, and normalised vertical fluxes of momentum and heat on the gradient Richardson number, Ri. Due to the large-scale IGW, these dependencies lose their universality. The maximal value of the flux Richardson number (universal constant ≈0.2–0.25 in the no-IGW regime) becomes strongly variable. In the vertically homogeneous stratification, it increases with increasing wave energy and can even exceed 1. For heterogeneous stratification, when internal gravity waves propagate towards stronger stratification, the maximal flux Richardson number decreases with increasing wave energy, reaches zero and then becomes negative. In other words, the vertical flux of potential temperature becomes counter-gradient. Internal gravity waves also reduce the anisotropy of turbulence: in contrast to the mean wind shear, which generates only horizontal TKE, internal gravity waves generate both horizontal and vertical TKE. Internal gravity waves also increase the share of TPE in the turbulent total energy (TTE = TKE + TPE). A well-known effect of internal gravity waves is their direct contribution to the vertical transport of momentum. Depending on the direction (downward or upward), internal gravity waves either strengthen or weaken the total vertical flux of momentum. Predictions from the proposed model are consistent with available data from atmospheric and laboratory experiments, direct numerical simulations and large-eddy simulations.