During the last decades, an ongoing increase in forest coverage has been observed in most European mountain areas, where traditional farming and agriculture have been abandoned. The aim of this study was to develop a fine-scale model of the fate of forest coverage over a broad area over the next 50 to 100 years to assist the planning efforts of conservation managers of Paneveggio Nature Park, Italy. This work shows that the application of a fine-scale, spatially explicit Markov chain (MC) model, together with a longitudinal dataset (forest coverage from 1859 to 2006), allowed statistically accurate projections and a likely spatial prediction of forest coverage while offering insights directly applicable to management practices. The results predict an increase in forest surface area and a decrease in fragmentation, with a consequent loss of open habitats that are a priority for the conservation of biodiversity. This protocol, if applied to other areas, can be used for designing long-term management measures with a focus on habitats where conservation status is at risk.