EEPSEA funds cross-country researchers through a closed call for proposals on key research areas. Researchers involved in such projects meet to set common objectives, develop a common framework, and agree on common research instruments to be used. Below is a list of ongoing EEPSEA cross-country research projects
| Title | Details |
| Intra-Household Impacts of Climate Hazards in Coastal Communities: A Cross Country Perspective | Project leader: Asa Jose U. Sajise, University of the Philippines Los Baños Countries: Cambodia, Philippines, Vietnam |
| Valuation of Ecosystem Functions and Services Provided by Mangrove Ecosystems in Southeast Asia: Literature Review and Assessment | Project leader: Pham Khnah Nam, University of Economic Ho Chi Minh City Countries: Malaysia, Indonesia, Vietnam, Philippines, Thailand |
| Documentation of Existing Cases of Payment for Environmental Services (PES) | Project leader: Herminia A. Francisco, EEPSEA Countries: Philippines, Thailand, Cambodia, Lao PDR, Indonesia, Malaysia |