The Natura 2000 network is an ecological network covering the whole territory of the European Union to ensure the long-term maintenance of threatened or rare natural habitats and species of flora and fauna, including in metropolitan and rural areas. Some of the Natura 2000 sites have been subject to changes in ownership that have led to a fragmentation of the territory. Private entities may own areas within a Natura 2000 site and must ensure sustainable management of their property, especially from an ecological point of view. The case study is the Stellantis–La Mandria site, a private area owned by Stellantis, within the Natura 2000 site “ZSC IT1110079 La Mandria”, near Turin. The research proposes a participatory methodology, mainly addressed in this first phase to experts and professionals and aimed at the valorisation and management of private Natura 2000 sites previously considered as industrial sites, to allow a careful fruition and safeguarding of the natural heritage. The aim of the research is to provide a methodological approach and the first qualitative results useful to providing the owners with an indication for a more targeted management of the site; mapping the areas that provide ecosystem services (ES, especially cultural ones); mapping the areas that could be subject to future fruition; collaborating with the managing body to collect useful data for the future drafting of a new area plan. Two main research activities were carried out, a SWOT (strengths, weaknesses, opportunities, and threats) analysis concerning the management and possible future fruition of the site and a participatory mapping of ES. It should be emphasised that the research allowed the first results to be obtained, which, on the one hand, make it possible to validate the methodology used to achieve the objectives and, on the other hand, the results will have to be implemented over time by involving numerous stakeholders among those who can access the private area. The results of the research highlight opportunities and threats with regard to the conservation of ecological–environmental characteristics and future fruition of the site. The participatory mapping identifies areas with different ecological value and, therefore, different management needs and identifies areas that could be used differently for future fruition. Overall, the results aim to meet some of the European Commission’s wishes regarding Natura 2000 sites, with particular reference to the involvement of different stakeholders and experts for the conservation of biodiversity and the integration of ecological and social aspects into the management and fruition plans.