Here we analyze the impact of four planetary boundary-layer (PBL) parametrization schemes from the Weather Research and Forecasting (WRF) numerical weather prediction model on simulations of meteorological variables and predicted pollutant concentrations from an air quality forecast system (AQFS). The current setup of the Spanish operational AQFS, CALIOPE, is composed of the WRF-ARW V3.5.1 meteorological model tied to the Yonsei University (YSU) PBL scheme, HERMES v2 emissions model, CMAQ V5.0.2 chemical transport model, and dust outputs from BSC-DREAM8bv2. We test the performance of the YSU scheme against the Assymetric Convective Model Version 2 (ACM2), Mellor-Yamada-Janjic (MYJ), and Bougeault-Lacarrère (BouLac) schemes. The one-day diagnostic case study is selected to represent the most frequent synoptic condition in the northeast Iberian Peninsula during spring 2015; regional recirculations. It is shown that the ACM2 PBL scheme performs well with daytime PBL height, as validated against estimates retrieved using a micro-pulse lidar system (mean bias = − 0.11 km). In turn, the BouLac scheme showed WRF-simulated air and dew point temperature closer to METAR surface meteorological observations. Results are more ambiguous when simulated pollutant concentrations from CMAQ are validated against network urban, suburban, and rural background stations. The ACM2 scheme showed the lowest mean bias (− 0.96 μg m− 3) with respect to surface ozone at urban stations, while the YSU scheme performed best with simulated nitrogen dioxide (− 6.48 μg m− 3). The poorest results were with simulated particulate matter, with similar results found with all schemes tested.