The microscale model WINDIE, initially developed for the simulation of neutral atmospheric flows over complex topography, is here extended to the study of stratified atmospheric flows with Coriolis effects, with particular focus on its application to wind farm development projects. The code now uses E–l and E– ϵ–l turbulence models, which have shown to be more adequate than the standard E– ϵ model for the simulation of atmospheric flows. The validation tasks include 1D atmospheric boundary layers from the first two cases produced by the Global Energy and Water Cycle Experiment Atmospheric Boundary Layer Study: a stably stratified boundary layer and a diurnal-cycle over land, respectively. To test the applicability of the new code to real situations, a series of simulations were performed of the time-varying atmospheric flow (a 3-month period between February and May 2012) over a moderately complex topography in the Portuguese mainland, using the Weather Research and Forecasting with Advanced Research WRF (WRF-ARW) mesoscale code on a 3 km mesh to produce time-varying boundary conditions for the microscale code, in a dynamic coupling fashion. Comparisons with sonic anemometer measurements at the hill top and with WRF-ARW results from a finer horizontal resolution mesh ( Δx,y = 1 ∕ 3 km) showed that the code can adequately simulate real atmospheric flows over complex topography. Copyright © 2014 John Wiley & Sons, Ltd.