The seeming dichotomy between the protection of biodiversity and the supply of ecosystem services (ESs) represents an outstanding field of research that requires a structured and detailed analysis. The paper analyzes and discusses the role of ESs within spatial planning and strategic environmental assessment (SEA) procedures through the content analysis methodology and a logical framework (LF) implemented into the SEA of municipal masterplans (MMPs). We discuss the role of ESs as factors that improve the effectiveness of SEA-based processes related to management plans (MPs) of sites that belong to the Sardinian Natura 2000 Network with reference to their positive impacts on environmental quality. The empirical outcomes put in evidence the inconsistencies between MMPs and MPs in terms of sustainability-oriented objectives and potential losses of the ESs productive output due to measures adopted by the MPs in order to protect habitats and species. The scant attention paid to ESs in the operational context of MMPs, MPs and SEA reports, particularly as regards their regulative framework, entails that the issue of the protection of ESs has to be carefully taken into account within the process of the definition and establishment of MPs through an SEA report that integrates the MPs and MMPs LFs.