Sustainable use of biodiversity and ecosystem services are among the key agendas of the UN Sustainable Development Goals (SDGs)(CBD 2014; UNEP. IRD 2016; Wood et al. 2018). To pursue this, the core research agendas for sustainability science include the following:(1) co-designing future scenarios and visions of social–ecological system with a participatory approach,(2) integrating indigenous and local knowledge (ILK) systems into both scientific knowledge and future scenarios of biodiversity and ecosystem services, and (3) the formulation of actions to transform society toward a more sustainable future (Miller et al. 2014; Schneider and Rist 2014; Kishita et al. 2016). In 2016, the fourth plenary of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES) approved a summary for policy makers of the methodological assessment of scenarios and models of biodiversity and ecosystem services. The report defined ‘‘scenarios’’as representations of possible futures for one or more components of a system, such as for drivers of change in nature and nature’s benefits, and alternative policy or management options. Likewise,‘‘models’’were defined as qualitative or quantitative descriptions of key components of a system and of the relationships that exist between those components. This report advocates for widespread use of scenarios to resolve the uncertainties in decision-making process, and further guides scientists and experts regarding the use of scenarios and models in the assessment of biodiversity and ecosystem services. Particularly, IPBES has identified the development of scenarios as a key to aid decision makers in identifying potential implications of different policy options, and to choose a desired path for future transition. Nevertheless, despite widespread advocacy, the current scientific disclosure evidently lacks long-term scenario approaches (Kok et al. 2017). Moreover, to reflect the future socio–ecological dynamics of biodiversity and ecosystem services, IPBES also emphasized the integration of ILK into the scenario building process, by engaging the substantial diversity of local contexts through participatory processes. To meet this challenge, the authors launched a new project in 2016 named ‘‘Predicting and Assessing Natural Capital and Ecosystem Service (PANCES)’’. The aim of this project is to develop an integrated assessment of social–ecological systems to predict and assess natural and socio-economic values of natural capital and ecosystem services in Japan under plausible alternative scenarios (including differing socio-economic conditions and policy options)(PANCES website: http://pance s. net/top/). PANCES also promotes multilevel governance of natural capital to maintain and improve ‘‘inclusive wellbeing’’and demonstrate the integrated assessment model at both national and local scales, with implications in Japan and beyond.