Electricity supply transition to reach carbon neutrality in Europe is expected to bring air quality and health co-benefits, but their regional distribution has not been investigated in detail. This study quantifies these co-benefits for 250 European electricity scenarios in 2035 across 296 sub-national regions. The study links a spatially-explicit electricity sector model with an air quality and health impact model and then accounts for susceptibility and vulnerability of populations to adverse health effects. In case of low-carbon transition, direct PM2.5 concentrations attributable to European electricity generation in 2035 could be reduced by 45–99% compared to a system with the generation capacities of 2018. Depending on the system’s make-up, health co-benefits can vary significantly, as does their regional distribution. Focus on the minimum system costs leads to 15 times higher continent-wide excess deaths and to higher regional inequality than the scenario with minimum air pollutant emissions, which would almost entirely eliminate PM2.5-related mortality attributable to electricity generation. The most vulnerable regions (Balkans, Northern Germany, Southeast France, and the West Midlands in England) would benefit from higher air quality co-benefits than the continental average.