Use of renewable energies has been promoted in Japan to meet the Paris agreement. However, the unplanned introduction of renewable energies, such as solar power and woody biomass energy, can cause conflicts among energy production, biodiversity, and ecosystem services (BES). In this study, we conducted a scenario analysis of land use management and the selection of renewable energy alternatives to identify such potential conflicts. The case study area was the Bekanbeushi River Watershed in the northeastern Japan. In this watershed, major industries include fishery, forestry, and pasture grass production for dairy farming. However, the population of workers in the primary industry has continuously decreased since 1960. The expansion of abandoned pastureland is considerable issue in this area. In this study, we defined this trend as business as usual scenario. Two alternative scenarios were set to utilize those abandoned pasture lands according to the regional energy plans. One scenario promoted the introduction of the solar power plant on the abandoned pasturelands. The other scenario utilized the production of woody biomass from pioneer species which established on the abandoned pasturelands. The LANDIS-II NECN succession was applied to express the plausible scenarios. And the simulation duration was from 2016 to 2100. The balance of regional energy demand and renewable energy supply, and a habitat suitability index for Blakiston’s fish owl, the Satoyama Index were calculated. Moreover, ecosystem services were estimated using the NEE, timber and pasture grass yield, and landscape change. Using those results, we evaluated the energy balance and detected the potential conflicts among renewable energy production and BES. This quantitative, spatially explicit and dynamic ecosystem impact assessment will contribute to the regional stakeholder’s decision making for implementing sustainable renewable energy in harmony with nature.