One challenge in the implementation of Long-Term Socio-Ecological Research (LTSER) is the consideration of relevant spatial and temporal scales. Mismatches between the scale(s) on which biodiversity is monitored and analysed, the scale(s) on which biodiversity is managed, and the scale(s) on which conservation policies are implemented have been identified as major obstacles towards halting or reducing biodiversity loss. Based on a meta-analysis of 18 biodiversity studies and a literature review, we discuss here a set of methods suitable to bridge the various scales of socio-ecological systems. For LTSER, multifunctionality of landscapes provides an inevitable link between natural and social sciences. Upscaling approaches from small-scale domains of classical long-term biodiversity research to the broad landscape scale include landscape metrics and spatial modelling. Multidisciplinary, integrated models are tools not only for linking disciplines but also for bridging scales. Models that are capable of analysing societal impacts on landscapes are particularly suitable for interdisciplinary biodiversity research. The involvement of stakeholders should be an integral part of these methods in order to minimise conflicts over local and regional management interventions implementing broad-scale policies. Participatory approaches allow the linkages between the specific scale domains of biodiversity, its management and policies.