Increasing human populations in urban areas pose a threat to species’ persistence through habitat loss and fragmentation. It is therefore essential that we develop methods to investigate critical habitat loss thresholds and least detrimental landscape configurations. We develop a framework to assess how the pattern of habitat loss impacts the ecological and social characteristics of a landscape and how this varies depending on the species and criteria by which it is judged. We use a scenario-based approach to test six propositions in which habitat is lost preferentially based on patch characteristics. We use eight bird and two amphibian species as indicator species. To compare scenarios, we present a method combining the output from a metapopulation model with measures of social impacts of land-cover change in a multiple criteria decision analysis. We also determine whether a habitat loss threshold exists, below which small loss of habitat can lead to large loss of species’ occupancy. We found that, of the scenarios presented, preferentially losing common habitats and smaller patches was least detrimental for both ecological and social factors. Threshold effects were found for all but the generalist bird species. We have outlined a workflow which allows for transparent, repeatable comparison between landscapes. This workflow can be used to compare urban landscape plans, or to develop general understanding of the impacts of different forms of habitat loss. Reassuringly, the recommendations based on the scenarios presented are in keeping with received conservation wisdom: to prioritise larger and/or rarer patches.