Fragmented natural habitats, such as old-growth forests, have been often considered island-like systems. However, whereas the isolation of real islands is mostly a function of their spatial arrangement, the biodiversity of old-growth forest patches is also affected by how well the surrounding suboptimal habitats, such as younger forests, can support the functional connectivity between the old-forest fragments. The latter topic remains largely unclear due to the lack of mechanistic knowledge about the processes behind species’ affinity for old forest. Although in animal ecology, functional connectivity has often been investigated with mechanistic agent-based models, these have rarely been applied for passively dispersing organism groups. We used a pattern-oriented modeling approach by combining a spatially explicit agent-based model and an empirical biodiversity dataset of Estonian old-growth nemoral forest sites, to study how forests of different ages between the old-forest fragments are exploited by different passively or slowly dispersing functional groups. We found that the establishment of ground layer vegetation, epiphytes, ectomycorrhizal and pathogenic fungi is significantly restricted in the younger forests, whereas no clear difference between forest-age classes emerged for survival. Our results thus suggest that establishment, not survival, is the main process behind the species’ affinity for old forest, concurring with studies that have demonstrated the importance of suitable microhabitat availability in older forests. We conclude that young secondary forests do not support the connectivity – and consequently, biodiversity – of many old-forest specific groups.