A failure to address social concerns in biodiversity conservation can lead to feelings of injustice among some actors, and hence jeopardize conservation goals. The complex socio-cultural and political context of the Calakmul Biosphere Reserve, Mexico, has historically led to multiple biodiversity conflicts. Our goal, in this case study, was to explore perceptions of justice held by local actors in relation to biodiversity conflicts. We then aimed to determine the following: 1) people's definitions of their feelings of justice; 2) the criteria used in this assessment; 3) variability in the criteria influencing them; and 4) implications for environmental management in the region and beyond. We worked with five focus groups, exploring three examples of biodiversity conflict around forest, water and jaguar management with a total of 41 ranchers, farmers and representatives of local producers. Our results demonstrated that people constructed their feelings of justice around four dimensions of justice: recognition (acknowledging individuals' rights, values, cultures and knowledge systems); ecological (fair and respectful treatment of the natural environment), procedural (fairness in processes of environmental management), distributive (fairness in the distribution of costs and benefits). We identified a list of criteria the participants used in their appraisal of justice and sources of variation such as the social scale of focus and participant role, and whom they perceived to be responsible for resource management. We propose a new framework that conceptualizes justice-as-recognition and ecological justice as forms of conditional justices, and procedural and distributive justices as forms of practical justice. Conditional justice allows us to define who is a legitimate source of justice norms and if nature should be integrated in the scope of justice; hence, conditional justice underpins other dimensions of justice. On the other hand, procedural and distributive address the daily practices of fair processes and distribution. We propose that the perception of justice is a neglected but important aspect to include in integrative approaches to managing biodiversity conflicts. Addressing demands of justice in environmental management will require us to consider more than the distribution of costs and benefits among actors. We also need to respect the plurality of fairness perspectives and to recognize the benefits of dialogical approaches to achieve more successful environmental management.