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Population-decline and subsequent underuse of social-ecological landscapes are increasingly being recognized as one of the crucial drivers behind the loss and deterioration of biodiversity and ecosystem services. In line with this, the study aimed to explore how alternative development pathways influence future land-use patterns, biodiversity and ecosystem services against a rapidly declining population in the Noto peninsula of Japan. By combining land-use simulation and evaluation of ecosystem services, the study formulated four exploratory scenarios for 2050, assuming a contrasting level of the society’s reliance on domestic natural capital and different demographic patterns. At first, we analyzed historical land-use changes between 1997 and 2007 and thereby simulated four plausible alternative scenarios using the Multi-Layer Perceptron Neural Network model. These scenarios were further used to quantify ecosystem services and landscape heterogeneity (as biodiversity indicator). The scenario analysis demonstrated that future land-use pattern could vary drastically depending on how the society utilize local natural capital even under the severe depopulation trend, whereas demographic patterns, in general, did not make discernible differences in land-use, biodiversity and ecosystem services. Nevertheless, a land-use change made considerable differences in the level of ecosystem services and landscape heterogeneity with varying degrees. Our analysis suggested that ecosystem services such as food production and nitrogen retention as well as landscape heterogeneity would decrease considerably by 2050 under the scenarios where the utilization of local natural capital decline and a significant amount of farmland are abandoned. Our findings highlight the vital role of land-use and agricultural policy in shaping the future availability of ecosystem services and biodiversity in this area.