Changes in climate and land-use may elicit an increased emission of allergenic pollen amounts in the air, causing a rise in respiratory allergies and affecting public health more than previously thought. Here we have used a well-established pollen transport model SILAM (System for Integrated modeLling of Atmospheric coMposition) for attributing the long-term changes in airborne pollen concentrations of birches and grasses to climate change and vegetation dynamics. The pollen transport model is applied for Belgium and is driven by ECMWF ERA5 meteorological data (European Centre for Medium-Range Weather Forecasts, fifth generation of ECMWF atmospheric reanalysis of the global climate). The dynamic vegetation components of the model are based on multi-decadal datasets for 1982–2019 on spatially distributed birch and grass pollen emission sources. For each model gridcell we have computed the change rate of the seasonal birch and grass pollen cycles based on daily pollen concentrations, and of the daily meteorological model input. Finally, the gridcell based association between trends in pollen and climate change are derived. Our findings show that during the period 1982–2019 a strong increase in birch pollen concentrations is associated with increasing radiation, decreasing precipitation and decreasing horizontal wind speed near the surface. A strong decrease of grass pollen concentrations over time is driven by a decreasing trend in grass pollen sources, and it is also associated with decreasing precipitation. The magnitude of the associations between meteorology and airborne birch pollen concentrations are almost twice the association between meteorology and grass pollen, and the spatial variations are substantial even on the scales of small countries. The specific contribution of birch tree and pollen production dynamics to the concentrations of birch pollen in the air over time is highly associated with wind speed and precipitation. Introducing the inter-seasonal variation in birch pollen production during the period 1982–2019 intensifies the climate induced increase of airborne birch pollen concentrations with ∼6%. In contrast, the grass pollen production dynamics resulted into ∼10 times less grass pollen over the studied period compared to climate change effects.