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Abstract Accurate microscale flow simulations are essential for assessing wind characteristics in complex terrain. This study evaluates a large ensemble of multiscale simulations, including large‐eddy simulations (LES), using the Weather Research and Forecasting model (WRF) over Perdigão, Portugal, driven by boundary conditions from multiple global data sets. Simulations are compared with data from the Perdigão field campaign, including radiosonde and flux tower measurements. Results show that LES, using high‐resolution topography and land use data, better replicate flow features and dynamics, providing valuable insights for wind resource quantification and mapping. We identify that model performance varies spatially. The RMSE of wind speed at 10 m at ridge towers is 5.65 m , while at valley towers, it is lower (2.28 m ), and variation across runs is greater for higher wind speeds. Temporally, surface winds show substantial variability throughout the day, posing greater modeling challenges during nighttime and synoptic transitions. This variability is not observed at 100 m, where topographic effects are less dominant and RMSE remains consistent across runs. Simulations driven by hourly boundary conditions perform best. However, drawing general conclusions about optimal turbulence modeling in the gray zone remains challenging due to microscale meteorology in complex terrain. Wind field characteristics are sensitive to turbulence scheme choice, particularly in the boundary layer, while above it, wind behavior is mainly influenced by boundary conditions. These results help identify key factors driving model variability and biases, which may guide future model developments to enhance wind flow simulation accuracy and reliability.