The System of Environmental-Economic Accounting Experimental Ecosystem Accounting (SEEA EEA) represents a crucial approach to incorporate the assessment of the sustainable use of natural resources and ecosystems into decision- and policy-making. However, its application is constrained by challenges distinct across specific implementation contexts, including those present in developing nations. In this paper, we focus on a pilot SEEA EEA application in a local-scale case study in Kyzyl Unkur, Jalal-Abad region, the Kyrgyz Republic, characterized by a unique natural walnut forest. We summarize key methodological and empirical challenges identified through collaboration with local experts and stakeholders during the compilation of Supply and Use tables for selected ecosystem services (ES) relevant at local, national and global levels. Specifically, we focus on the methodological challenges related to a) defining and assigning benefits for own consumption; b) delineating the chain of ES flows (e.g., fodder for farm animals); c) uncovering the relevance of carbon sequestration in developing nation contexts which are often minor greenhouse gas (GHG) emitters and demand for the service lies mostly beyond their boundaries. Among empirical challenges, we highlight the issues of data collection and availability. The aim of this communication is to provide lessons learnt from building SEEA EEA accounts in a developing, data-scarce context, potentially transferable to other similar applications.