The role of bioenergy in climate change mitigation is a topic of heated debate, as the demand for land may result in social and ecological conflicts. Biodiversity impacts are a key controversy, given that biodiversity conservation is a globally agreed goal under pressure due to both climate change and land use. Impact assessment of bioenergy in various socio-economic and policy scenarios is a crucial basis for planning sound climate mitigation policy. Empirical studies have identified positive and negative local impacts of different bioenergy types on biodiversity, but ignored indirect impacts caused by displacement of other human activities. Integrated assessment models (IAMs) provide land-use scenarios based on socio-economic and policy storylines. Global scenarios capture both direct and indirect land-use change, and are therefore an appealing tool for assessing the impacts of bioenergy on biodiversity. However, IAMs have been originally designed to address questions of a different nature. Here, we illustrate the properties of IAMs from the biodiversity conservation perspective and discuss the set of questions they could answer. We find IAMs are a useful starting point for more detailed regional planning and assessment. However, they have important limitations that should not be overlooked. Global scenarios may not capture all impacts, such as changes in forest habitat quality or small-scale landscape structure, identified as key factors in empirical studies. We recommend increasing spatial accuracy of IAMs through region-specific, complementary modelling, including climate change into predictive assessments, and considering future biodiversity conservation needs in assessments of impacts and sustainable potentials of bioenergy.