Street trees provide many positive ecosystem services, especially improving thermal comfort for cities in temperate climate in summer. However, trees also emit biogenic volatile organic compounds (BVOC), most abundant of which is isoprene. Isoprene is a reactive compound and plays an important role in ozone and secondary organic aerosol formation, thus negatively impacting urban air quality. Isoprene emission is dependent on the biophysical factors such as leaf temperature, short wave radiation, soil moisture, tree age, and leaf area index (LAI). In addition, urban street trees are known to modify the microclimate through radiative heat exchanges and evapotranspiration. Therefore, the emission of isoprene depends on the microclimate of the environment, which could also be modified by themselves. However, the effect of tree-modified street-canyon microclimate on isoprene emissions has not been well understood and quantified. This is partly due to the lack of modeling tools to represent the interactions between trees, microclimate, and the biophysically-dependent emission process. Therefore, we couple a single-layer urban canopy model (SLUCM), which represents the modification of surface energy exchanges by trees, to the Model of Emissions of Gases and Aerosols from Nature (MEGAN) in this work. Comparisons between coupled SLUCM-MEGAN with MEGAN that is directly forced by meteorological quantities from reanalysis are made. Results show that the coupled SLUCM-MEGAN model predicts a lower emission activity factor than the uncoupled approach. Although high sensible heat flux in the street canyons increases the daytime temperature more than the reanalysis data, the dominant control on the isoprene emission factor is still shortwave radiation. The discrepancy between the shortwave radiation in the two models accounts for isoprene emission factor from SLUCM-MEGAN being lower than directly forced MEGAN data. At night, street canyons generally have a lower air and leaf temperatures than air temperature in the boundary layer as sensible heat flux becomes negative. The coupled and uncoupled models are applied to a typical neighborhood in New York City and SLUCM-MEGAN shows lower predictions of the isoprene activity factor according to summer averaged maxima. Thus, the effect of street canyon microclimate on emissions can contribute to uncertainties in BVOC emissions in air quality modeling in cities. Future work involves validating the coupled model using observations and quantifying tree planting strategies that improve thermal comfort while reducing isoprene emissions. Furthermore, it would be helpful to understand the spatial and temporal evolution of emitted isoprene in canopy environments that can be achieved by coupling SLUCM-MEGAN with the Large Eddy Simulation-Lagrangian Stochastic Model (LES-LSM).