Biogenic volatile organic compound (BVOC) emissions are one of the essential inputs for chemical transport models (CTMs), but their estimates are associated with large uncertainties, leading to significant influence on air quality modelling. This study aims to investigate the effects of using different BVOC emission models on the performance of a CTM in simulating secondary pollutants, i.e. ozone, organic, and inorganic aerosols. European air quality was simulated for the year 2011 by the regional air quality model Comprehensive Air Quality Model with Extensions (CAMx) version 6.3, using BVOC emissions calculated by two emission models: the Paul Scherrer Institute (PSI) model and the Model of Emissions of Gases and Aerosol from Nature (MEGAN) version 2.1. Comparison of isoprene and monoterpene emissions from both models showed large differences in their general amounts, as well as their spatial distribution in both summer and winter. MEGAN produced more isoprene emissions by a factor of 3 while the PSI model generated 3 times the monoterpene emissions in summer, while there was negligible difference ( ∼ 4 %) in sesquiterpene emissions associated with the two models. Despite the large differences in isoprene emissions (i.e. 3-fold), the resulting impact in predicted summertime ozone proved to be minor (<10 %; MEGAN O3 was higher than PSI O₃ by ∼ 7 ppb). Comparisons with measurements from the European air quality database (AirBase) indicated that PSI emissions might improve the model performance at low ozone concentrations but worsen performance at high ozone levels (>60 ppb). A much larger effect of the different BVOC emissions was found for the secondary organic aerosol (SOA) concentrations. The higher monoterpene emissions (a factor of ∼ 3) by the PSI model led to higher SOA by ∼ 110 % on average in summer, compared to MEGAN, and lead to better agreement between modelled and measured organic aerosol (OA): the mean bias between modelled and measured OA at nine measurement stations using Aerodyne aerosol chemical speciation monitors (ACSMs) or Aerodyne aerosol mass spectrometers (AMSs) was reduced by 21 %–83 % at rural or remote stations. Effects on inorganic aerosols (particulate nitrate, sulfate, and ammonia) were relatively small (<15 %).