The available resources for biodiversity conservation are so chronically limited that conservation planners must choose what to protect and what to leave for the future. This implies not only the choice of areas or species requiring protection, but also what to protect first; that is, design a conservation schedule. Scheduling is the coordination of actions over time and space depending on the urgency for intervention, the spatial options for protecting features, the availability of funds, and other factors. Because most of these factors are poorly known, several simplifications are commonly made when setting priorities. These simplifications, or assumptions, regard both the socio-economic and the ecological aspects of biodiversity conservation. The unreserved use of these assumptions can reduce the effectiveness of conservation actions. In my PhD project, I identified how assumptions affect the choice of prioritization approaches when scheduling conservation actions and suggested ways to overcome their negative effects by making use of sensitivity analyses and conservation scenarios. Secondly, I addressed some of these assumptions by explicitly considering the complexities ignored in conservation decision-making. My focus has been on assumptions related to the biodiversity responses to habitat loss and fragmentation, and the emerging properties of reserve networks that arise when addressing both habitat loss and connectivity. I have also investigated the robustness of conservation decisions to: (1) uncertainty about spatial predictions of threats to biodiversity; and, (2) assumptions about the ability of conservation actions to displace or mitigate these threats. Finally, I have demonstrated the value of using multiple scenarios to set conservation priorities by coupling multiple global land use and climate change scenarios with fine-scale habitat suitability models. I then used these scenarios and models to identify future conservation priorities for the world’s mammals in a range of possible futures. By testing different hypotheses and assumptions regarding the behaviour of existing techniques and suggesting new approaches for environmental decision making, this research has contributed to the theoretical advancement of the discipline. At the same time, the rules of thumb and recommendations on optimal priority setting for conservation practitioners stemming from my research are likely to have important practical consequences for conservation decisions at local to global scales.