Abstract Unsteadiness and horizontal heterogeneities frequently characterize atmospheric motions, especially within convective storms, which are frequently studied using large-eddy simulations (LES). The models of near-surface turbulence employed by atmospheric LES, however, predominantly assume statistically steady and horizontally homogeneous conditions (known as the equilibrium approach). The primary objective of this work is to investigate the potential consequences of such unrealistic assumptions in simulations of tornadoes. Cloud Model 1 (CM1) LES runs are performed using three approaches to model near-surface turbulence: the “semi-slip” boundary condition (which is the most commonly used equilibrium approach), a recently proposed nonequilibrium approach that accounts for some of the effects of turbulence memory, and a nonequilibrium approach based on thin boundary layer equations (TBLE) originally proposed by the engineering community for smooth-wall boundary layer applications. To be adopted for atmospheric applications, the TBLE approach is modified to account for the surface roughness. The implementation of TBLE into CM1 is evaluated using LES results of an idealized, neutral atmospheric boundary layer. LES runs are then performed for an idealized tornado characterized by rapid evolution, strongly curved air parcel trajectories, and substantial horizontal heterogeneities. The semi-slip boundary condition, by design, always yields a surface shear stress opposite the horizontal wind at the lowest LES grid level. The nonequilibrium approaches of modeling near-surface turbulence allow for a range of surface-shear-stress directions and enhance the resolved turbulence and wind gusts. The TBLE approach even occasionally permits kinetic energy backscatter from unresolved to resolved scales. Significance Statement The traditional approach of modeling the near-surface turbulence is not suitable for a tornado characterized by rapid evolution, strongly curved air parcel trajectories, and substantial horizontal heterogeneities. To understand the influence of statistically unsteady and horizontally heterogeneous near-surface conditions on tornadoes, this work adopts a fairly sophisticated approach from the engineering community and implements it into a widely used atmospheric model with necessary modifications. Compared to the traditional approach, the newly implemented approach produces more turbulent near-surface winds, more flexible surface-drag directions, and stronger wind gusts. These findings suggest a simulated tornado is very sensitive to the modeling approach of near-surface turbulence.