On a global scale, protected areas (PAs) are one of the main tools used for biodiversity conservation. However, accelerated biodiversity loss and lack of social acceptance of PAs call into question their ability to reach long-term biodiversity conservation objectives. To address this, conservation scientists and practitioners have moved from segregative to integrative models of PAs. When the segregative model sees PAs as human exclusion zones, the integrative model considers conservation and development projects and multiple partnerships with local stakeholders within and outside PAs. Given this paradigmatic evolution, a PA and its surrounding landscape are increasingly regarded as a single social-ecological system (SES). This development brings new challenges for conservationists: How should these complex and dynamic systems be managed, and how can their pathways be described and piloted? Using French nature reserves (NRs) as case studies, we propose a framework for analyzing the integration pathways of PAs within their social-ecological context. We identified the pathways of 10 NRs according to their degree of integration in the surrounding landscape (spatial), their management objectives (sectoral), and their governance systems (institutional). We analyzed these pathways using three metaphors associated with resilience thinking (adaptive cycle, adaptation, and transformation). We discussed how these 10 NRs have changed over time, revealing how practitioners anticipate future pathways and avoid undesirable states. Through an exploration of the totality of an SES’s spatial, sectoral, and institutional pathways, the framework we propose is a potential tool for identifying opportunities and constraints for long-term conservation actions.