Mapping the distribution of allergenic plants in urbanized landscapes is of high importance to evaluate its impact on human health. However, data is not always available for the allergy-relevant species such as alder, birch, hazel, especially within cities where systematic inventories are often missing or not readily available. This research presents an approach to produce high-resolution abundance maps of allergenic tree species using existing forest inventories and opportunistic open-access citizen science data. Following a two-step approach, we first built species distribution models (SDMs) to predict species habitat suitability, using environmental characteristics as predictors. Second, we used statistical regressions to model the relationships between abundance, the habitat suitability predicted by the SDMs, and additional vegetation cover covariates. The combination of forest inventory data with citizen science data improves the accuracy of abundance distribution models of allergenic tree species. This produces a continuous, 1-hectare resolution map of alder, birch, and hazel showing spatial variations of abundance distributions both within the urban fabric and along the urban–rural gradient. Species abundance modelling can offer a better understanding of the existing and potential future allergy risk posed by green spaces and pave the way for a wide variety of applications at fine-scale, which is indispensable for evidence-based urban green space policy and planning in support of public health.