Park managers in alpine areas must deal with the increase in forest coverage that has been observed in most European mountain areas, where traditional farming and agricultural practices have been abandoned. The aim of this study is to develop a fine-scale model of a broad area to support the managers of Paneveggio Nature Park (Italy) in conservation planning by focusing on the fate of priority areas for conservation in the next 50-100 years. GIS analyses were performed to assess the afforestation dynamic over time using two historical maps (from 1859 and 1936) and a series of aerial photographs and ortho-photos (taken from 1954 to 2006) covering a time span of 150 years. The results show an increase in the forest surface area of about 35%. Additionally, the forest became progressively more compact and less fragmented, with a consequent loss of ecotones and open habitats that are important for biodiversity. Markov chain-cellular automata models were used to project future changes, evaluating the effects on a habitat scale. Simulations show that some habitats defined as priority by the EU Habitat Directive will be compromised by the forest expansion by 2050 and suffer a consistent loss by 2100. This protocol, applied to other areas, can be used for designing long-term management measures with a focus on habitats where conservation status is at risk.