Nitrogen deposition threatens Portugal’s ecosystems. According to current assessments, there is no improvement ahead, despite the major emission reductions planned until 2030. These ecosystems remain at risk because research and policy support capacity are lacking. Through strategic research partnerships, the EU-funded FONDA project aims to boost the University of Aveiro’s expertise in modelling and mapping reactive nitrogen compounds’ emissions, transport, transformation and deposition. Innovative education and advanced training programmes will foster a new generation of researchers. In addition, a sustainable innovation framework will enable long-term, strategic collaboration. The University of Aveiro will ultimately become a leader in the air quality modelling field.