Quantifying the co-benefits of renewable energy investments can aid policymakers in identifying technologies capable of generating significant social, economic, and environmental benefits to effectively offset mitigation costs. Although there has been a growing body of work evaluating co-benefits, few studies have compared the potential co-benefits of several technologies across different regions in key countries. This study fills this gap by formulating a new modeling structure to assess the environmental–health–economic co-benefits of hybrid renewable energy systems (HRESs) in different parts of Indonesia. The proposed model is unique in that it incorporates various techno-economic activities to assess air quality, health, and economic benefits and then presents results as part of a cost–benefit analysis. From the intervention scenario, the modeling results show that installing 0.5 GW grid-connected solar PV, 100 MW of wind turbines, and a 100 MW biomass generator to cover a total of 1.64 million residential load units in the Bali province can avoid GHGs, PM_2.5, disability-adjusted life years (DALYs), and provide health savings of 1.73 Mt/y, 289.02 t/y, 1648, and 6.16 million USD/y, respectively. In addition, it shows that the payback period is enhanced by one year, while the net present value is increased by 28%. In Jakarta, a 3 GW solar PV plant and a 100 MW biomass generator that supply 5.8 million residential load units can deliver 32,490 averted DALYs and 652.81 million USD/y of health care savings. Nationally, the contribution of renewable energy to the electricity supply mix could grow from the 2020 baseline of 18.85% to 26.93%, reducing dependence on oil and coal contribution by 5.32%.