West Africa, already highly influenced by the negative effects of climate change, is additionally characterized by rapid population growth, endemic poverty, and insecurity. This is affecting the natural capital of its ecosystems and the services they provide. Natural capital accounting (NCA) provides the fundamental evidence base required for informing economics and environmental decisions, thus strengthening the conservation and management of natural resources. The objective of this study is to showcase the development and evaluation of a semi-automated NCA platform (Sys4ENCA) designed to support decision making in the context of protected areas management in a multi-level example in western Africa. The accounting results highlight that simulations at the broader scale using national public data show that the natural capital of ecosystems in western Africa depends strongly on the mean climate and its variability. Evaluating regional datasets, the simulation with the platform shows that pressure on land in combination with weak governance reduces the capability of the ecosystem to deliver the required services in a sustainable manner, i.e., in the eastern part of the Bafing-Falémé landscape, where mining and intensive agriculture are fueling loss of natural capital. The results of Tier-3 accounting using local datasets enhanced the spatial variability and highlighted additional hotspots of degradation compared to the regional results, i.e., the prospective construction of a hydro-electricity dam (Koukoutamba) in the southern part of the Moyen-Bafing National Park located in the Bafing-Falémé landscape. The Sys4ENCA platform, combined with a multi-level approach, showed itself to be a valuable tool to facilitate protected area management as it provides not only consolidated information at a local scale but also the broader context and external pressures, i.e., climate change and demand for land. Given its automatized nature, the platform reduces human errors and increases the efficiency, speed, and harmonisation of computation over long timeframes and spatial scales.