<p>Factoring clean air and health co-benefits into urban climate plans can reduce cost concerns and build multi-stakeholder support for net-zero transitions. Most of the research estimating these co-benefits has focused on large cities. Limited research has concentrated on small- and medium-sized cities. Small- and medium-sized cities merit more attention since they tend to have different energy and industrial structures and less technical capacity to estimate co-benefits than larger cities. This paper therefore demonstrates how differences in these structures and other contextual factors influence the co-benefits from net-zero transport, energy, industry and waste policies in two small- to medium-sized cities in Japan: Hachinohe city and Niigata city. More concretely, the paper used the Greenhouse gas–Air pollution Interactions and Synergies (GAINS) model to estimate CO₂ and PM_2.5 emission under business-as-usual (BAU) and net-zero scenarios from 2013 to 2050. The modelling demonstrates that CO₂ could fall by approximately 46% in 2030 and 95% by 2050 in the two studied cities under net-zero scenarios. The modelling further shows that PM_2.5 could also reduce by approximately 30% (2030) and 47% (2050) in Niigata city and by 38% (2030) and 54% (2050) in Hachinohe city under relevant net-zero scenarios. The accumulated lives saved from 2013 to 2050 moving from BAU scenario to net-zero scenario were 478 and 42 in Niigata city and Hachinohe city respectively. The results suggest that, even in cities with relatively clean air, the benefits of net-zero transitions are significant. Maximizing these benefits will require greater efforts to engage with policymakers in small and medium-sized cities to co-design solutions and scale healthy net-zero transitions.</p> Graphical abstract <p></p>