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Context: Montados are dynamic agroforestry systems of southern Portugal, with high economic and ecological values. Changes in land use and cover have important implications for landscape-level biodiversity and its conservation.Objectives: Our objectives were to evaluate the biodiversity values and trends in a montado system in the Alentejo, Portugal so as to inform landscape level conservation approaches. In doing so, we aimed to develop a replicable and robust approach drawing together field observation, expert opinion, and remote sensing to produce predictions relevant to land management planning.Methods: Field sampling and subsequent analysis of data on the birds, butterflies and plants in eight distinct land covers allowed the identification of two principal habitat groupings of importance: ‘montado mosaic’ and ‘shrubland’. Morphological spatial pattern analysis was performed on Landsat-derived GIS habitat layers for 1984 and 2009, generating maps and statistics for change in the different landscape functional classes. In addition, we demonstrated how the modelling of ecotones between open and closed biomes can identify the preferred hunting grounds of the threatened Iberian lynx and black vulture, flagship species whose conservation provides benefits to the area’s wider biodiversity values.Results: Total and core area of montado mosaics and shrubland increased over the 25 year period, whilst the amount of habitat connectivity declined in the case of shrubland. Considerable local variation in these trends highlighted targetable areas for conservation action (e.g. through agri-environment spending).Conclusions: A rapid and robust approach was demonstrated, with potentially wider utility for biodiversity assessment and planning. [ABSTRACT FROM AUTHOR]