Mesoscale simulations are typically performed at coarse resolutions that do not adequately represent underlying topography; nesting large-eddy simulations within a mesoscale model can better resolve terrain and hence capture topographically-induced stable flow phenomena. In the case of the Mountain Terrain Atmospheric Modelling and Observations (MATERHORN) program, large temperature fluctuations were observed on the slope of Granite Peak, Utah, which partially encloses a cold-air pool in the east basin. These flow features are able to be resolved using large-eddy simulation within the Weather Research and Forecasting (WRF) model with $$\Delta x = 100$$ m, allowing accurate representation of lee vortices with horizontal length scale of $${\mathcal {O}}$$ (1 km). At this resolution, terrain slopes become quite steep, and some model warm biases remain in the east basin due to limits on terrain-following coordinates that prevent the model from fully resolving drainage flows with this steep terrain. A new timestep limit for the WRF model related to these steep slopes is proposed. In addition, the initialization of soil moisture is adjusted by drying the shallowest layer to assist the formation of a cold pool in the large-eddy simulation. These real case simulations compare well to observations and also to previously published simulations using idealized configurations to study similar phenomena. For instance, the values of non-dimensional mountain height, which characterize flow regimes in idealized studies, are similar in the real case.