Forests are becoming increasingly fragmented world-wide, creating forest patches with reduced area and greater exposure to human land uses along fragment edges. In this study, we predict the future impacts of anthropogenic edges and fragment size on the future occupancy of deadwood-dwelling fungi in boreal old-growth forest fragments. We used Bayesian models fitted to empirical data to predict 40years of occupancy dynamics of logs by a group of old-growth forest indicator fungi and two common fungi under different scenarios of clear-cutting in adjacent forest (0%, 25%, 50% and 100%) and fragment sizes (1-20ha). Small fragment size (1-3<bold></bold>14ha) and intensified forestry with 50-100% clear-cutting of forest around old-growth forest fragments lead to lower predicted occupancy of old-growth indicator fungi while common generalist species like Fomitopsis pinicola increased. There was a trade-off between fragment size and management, where increasing fragment size buffered the negative long-term effects from increased adjacent clear-cutting. These changes in fungal occupancy at the edge should be accounted for when working towards conservation targets for protected areas, such as the Aichi target 11.Synthesis and applications. Preserve what is left - but buffer for change. Small forest fragments often represent the last vestiges of high habitat quality (i.e. species, structures) in managed forest landscapes. As effective area-based conservation measures for the long-term occupancy of old-growth fungi, small fragments need to be managed to protect species from degrading transient edge effects. Management should focus on increasing the size of conservation areas with permanent buffer zones. Alternatively, non-simultaneous adjacent clear-cutting in a way that reduces the edge effect over time (i.e. dynamic buffers) may increase the effective area and improve performance of set-asides in protecting species of special concern for conservation. Preserve what is left - but buffer for change. Small forest fragments often represent the last vestiges of high habitat quality (i.e. species, structures) in managed forest landscapes. As effective area-based conservation measures for the long-term occupancy of old-growth fungi, small fragments need to be managed to protect species from degrading transient edge effects. Management should focus on increasing the size of conservation areas with permanent buffer zones. Alternatively, non-simultaneous adjacent clear-cutting in a way that reduces the edge effect over time (i.e. dynamic buffers) may increase the effective area and improve performance of set-asides in protecting species of special concern for conservation.