Biogenic volatile organic compounds (BVOCs) emitted from the natural ecosystem are highly reactive and can thus impact air quality and aerosol radiative forcing. BVOC emission models (e.g., Model of Emissions of Gases and Aerosols from Nature - MEGAN) in global and regional chemical transport models still have large uncertainties in estimating biogenic trace gases because of uncertainties in emission activity factors, specification of vegetation type, and plant emission factors. This study evaluates a set of updates made to MEGAN v2.04 in the Weather Research and Forecasting model coupled with chemistry (WRF-Chem version 3.9). Our study considers four simulations for each update made to MEGAN v2.04: (i) a control run with no changes to MEGAN, (ii) a simulation with the emission activity factors modified following MEGAN v2.10, (iii) a simulation considering the changes to the plant functional type (PFT) emission factor, and (iv) a simulation with the isoprene emission factor calculated within the MEGAN module instead of being prescribed by the input database. We evaluate two regions, Europe and the southeastern United States, by comparing WRF-Chem results to ground-based monitoring observations in Europe (i.e., AirBase database) and aircraft observations obtained during the NOMADSS field campaign. We find that the updates to MEGAN v2.04 in WRF-Chem caused overpredictions in ground-based ozone concentrations in Europe and in isoprene mixing ratios compared to aircraft observations in the southeastern US. The update in emission activity factors caused the largest biases. These results suggest that further experimental and modeling studies should be conducted to address potential shortcomings in BVOC emission models.