Forest management has altered forested environments and provoked stress to many natural habitats and biodiversity. The goal of biodiversity management is the long-term persistence of populations in human-modified environments. We demonstrate a spatio-temporal modeling approach to address the relationship between various management objectives and population persistence in the long-term in a commercial forest landscape. We used the flying squirrel (Pteromys volans), the three-toed woodpecker (Picoides tridactylus) and the long-tailed tit (Aegithalos caudatus) as example species. They are all forest species but they have distinctly different habitat requirements. In the model, forest growth, forest clearing and regional population dynamics were simulated and operated simultaneously. We addressed regional population persistence by varying the conservation goal: First, there are no obligations to protect the species. Second, forest stands where the species occur are not cleared. Third, the entire species' habitat is preserved. The general message from our analysis is that the sustainable area cleared annually depends on the species' habitat requirements, and species' responses to management have various time lags.