Here, we examine the use of a cell perturbation method to help improve the transition from coarse to fine scales. We consider a nested setup over the Perdigao valley, the site of the 2017 international field campain in Portugal. Using the Weather and Research Forecasting (WRF) model, we illustrate the challenges of the standard grid nesting procedure and compare it to results using the cell perturbation method. The perturbations are applied to the potential temperature field at the inflow boundaries of the nested domain and have shown to be successful in triggering smaller scales over flat terrain. Here, the method is applied to highly complex terrain for the first time. Results indicate that even over complex terrain, use of the perturbation method helps break down spurious streaky flow structures and enhances the turbulence spectra of the flow field at finer scales. The contributions of the perturbations are quantified to understand the need for these perturbations under varying flow conditions over complex terrain.