This paper aims to provide a comprehensive review of the literature on environmental conflicts within protected areas and identify key foundational theories to effectively study conflict phenomena. Through the lens of ecological economics, environmental conflicts are viewed as injustices rooted in the distribution of resource rights and power dynamics. Based upon the review, the paper proposes a novel theoretical framework that integrates principles from environmental justice and ecological economics to better outline the three dimensions of conflict: substance, process and relation. The framework conceptualises conflicts as social–ecological systems in which the configuration of social relations and entitlements over ecosystem services plays a pivotal role in understanding governance challenges related to resource management in protected areas. The paper also proposes a set of indicators to measure the theoretical domains. In line with the social–ecological systems approach, it underscores the importance of utilising social–ecological network analysis techniques to effectively calculate these indicators. Overall, the paper deliver a comprehensive toolkit for practitioners and policymakers in addressing the intricate dynamics of conflicts over natural resource management, especially within protected areas.