Air pollution and climate change are closely interlinked, once both share common emission sources, which mainly arise from fuel combustion and industrial processes. Climate mitigation actions bring co-benefits on air quality and human health. However, specific solutions can provide negative trade-offs for one side. The Portuguese Carbon Neutrality Roadmap was developed to assess conceivable cost-effective pathways to achieve zero net carbon emissions by 2050. Assessing its impacts, on air pollutant emissions, is the main focus of the present work. The bottom-up linear optimization energy system the integrated MARKAL-EFOM system (TIMES) model was selected as a modeling tool for the decarbonization scenarios assessment. The estimation of air pollutant emissions was performed exogenously to the TIMES model. Results show that reaching net zero greenhouse gas (GHG) emissions is possible, and technologically feasible, in Portugal, by 2050. The crucial and most cost-effective vector for decarbonizing the national economy is the end-use energy consumption electrification, renewable based, across all end-use sectors. Decarbonization efforts were found to have strong co-benefits for reducing air pollutant emissions in Portugal. Transport and power generation are the sectors with the greatest potential to reduce GHG emissions, providing likewise the most significant reductions of air pollutant emissions. Despite the overall positive effects, there are antagonistic effects, such as the use of biomass, mainly in industry and residential sectors, which translates into increases in particulate matter emissions. This is relevant for medium term projections, since results show that, by 2030, PM_2.5 emissions are unlikely to meet the emission reduction commitments set at the European level, if no additional control measures are considered.