The Natura 2000 network is the cornerstone of the EU Biodiversity Strategy aimed at halting the loss of biodiversity and ecosystem services. Yet in many EU Member States the level of development and execution of management plans and conservation measures of Natura 2000 sites is often very low due to scarce financial resources; for this reason management effectiveness is rarely achieved. This paper presents initial insights from the Life+ MGN project and highlights the costs and benefits associated with 2 out of 21 Natura 2000 study sites in Italy in order to present a new governance approach relying on the qualitative and quantitative valuation of Ecosystem Services (ES). Preliminary results suggest that the quantification of costs and benefits related to the Natura 2000 network is crucial for reaching Natura 2000 conservation objectives and measuring management effectiveness.