In this study, we present an improved framework for modelling isoprene emissions based on the latest version of the Model of Emissions of Gases and Aerosols from Nature (MEGAN). We use high resolution domain-specific tree cover data, species distributions, and species-specific emission factors, to update isoprene emission factors tailored to the Finnish boreal region. These modifications are implemented in MEGAN and integrated into the WRF-CHIMERE chemistry transport model, enabling a more accurate simulation of biogenic emissions. We perform simulations over three consecutive summer periods for the years 2017, 2018, and 2019. Our results reveal a significant reduction in bias for both isoprene emissions fluxes and concentrations compared to previous versions of MEGAN. We further evaluate a canopy correction model to account for the effects of forest canopy on vertical and horizontal transport of biogenic volatile organic compounds (BVOCs) concentrations. These adjustments additionally reduce the bias in modelled isoprene concentrations. The enhanced representation of isoprene emissions, and the effects of canopy on dispersion processes, both result in overall improvements of SOA formation and transportation, emphasizing the importance of ecosystem-specific modifications in emission models and the inclusion of forest canopy correction in chemical transport models. Our findings highlight the importance of moving beyond broad vegetation categories and incorporating detailed tree species distributions in emission factor calculations, demonstrating that ecosystem-specific adjustments are essential for realistic modelling of biogenic emissions and their impacts on atmospheric chemistry.