Investigation of the atmospheric boundary-layer structure in urban areas can be challenged by landscape complexity and the heterogenous conditions this instills. Stuttgart, Germany, is a city situated in a bowl-shaped basin and troubled by the accumulation of pollutants during weak-wind conditions. The center of Stuttgart is surrounded by steep slopes up to 250 m above the basin floor, except for an opening to the northeast that allows runoff towards the Neckar river. Urban planning and regulation of air quality require advanced monitoring and forecasting skills, which in turn require knowledge about the structure of the atmospheric boundary layer (ABL), down to the surface. Three-dimensional observations of the ABL were collected in the City Centre of Stuttgart in 2017. A laser ceilometer and a concerted network of Doppler lidar systems were deployed on roof-tops, providing continuous observations of the cloud base, the mixing-layer height and the three-dimensional wind field. The impact of weak-wind conditions, the presence of shear layers, properties of convective cells and the impact of nocturnal low-levels jets were studied for representative days in winter and summer. The observations revealed the development of distinctive layers with high directional deviation from the flow aloft, reoccurring as a dominant diurnal pattern. Our findings highlight the influence of topography and surface heterogeneity on the structure of the ABL and development of flow regimes near the surface that are relevant for the transport of heat and pollutants.