Achieving biodiversity targets will require acknowledging that human societies are highly interconnected with the biophysical life-support system, conforming social–ecological systems. Under the social–ecological systems framework, we recognize that human wellbeing depends, in part, upon ecosystems; additionally, biodiversity conservation depends on human behavior and governance. Precisely, under the social–ecological systems paradigm, three conservation challenges emerge: (1) to recognize the value pluralism of biodiversity in science and decision-making, (2) to acknowledge that social–ecological systems require institutional diversity to be managed effectively, and (3) to go beyond scientific disciplines towards a real transdisciplinary science. In this context, sustainability science emerges as the body of knowledge able to understand the complex interactions of social-ecological systems. Consequently, we argue that the current challenge of biodiversity conservation needs to be addressed through the operationalization of sustainability science along the three lines above.