Abstract Improvements to the Weather Research and Forecasting (WRF) Model are made to enable multiscale simulations over highly complex terrain with dynamically downscaled boundary conditions from the mesoscale to the microscale. Over steep terrain, the WRF Model develops numerical errors that are due to grid deformation of the terrain-following coordinates. An alternative coordinate system, the immersed boundary method (IBM), has been implemented into WRF, allowing for simulations over highly complex terrain; however, the new coordinate system precluded nesting within mesoscale simulations using WRF’s native terrain-following coordinates. Here, the immersed boundary method and WRF’s grid-nesting framework are modified to seamlessly work together. This improved framework for the first time allows for large-eddy simulation over complex (urban) terrain with IBM to be nested within a typical mesoscale WRF simulation. Simulations of the Joint Urban 2003 field campaign in Oklahoma City, Oklahoma, are performed using a multiscale five-domain nested configuration, spanning horizontal grid resolutions from 6 km to 2 m. These are compared with microscale-only simulations with idealized lateral boundary conditions and with observations of wind speed/direction and SF6 concentrations from a controlled release from intensive observation period 3. The multiscale simulation, which is configured independent of local observations, shows similar model skill predicting wind speed/direction and improved skill predicting SF6 concentrations when compared with the idealized simulations, which require use of observations to set mean flow conditions. Use of this improved multiscale framework shows promise for enabling large-eddy simulation over highly complex terrain with dynamically downscaled boundary conditions from mesoscale models.