When managing problem wildlife, we need to make decisions aimed to solve crises among factors of pressure (e.g. exotic species or communities), impacted targets (populations, communities, ecosystems, processes) and political and social pressures. These crises happen in multi-complex organizational, socio-ecological systems, often characterized from high uncertainty. Now, a large number of interdisciplinary conceptual tools, criteria and approaches, belonging to the problem-solving and decision-making arenas, is now available for practitioners and managers that work on conservation projects. In this review, we selected some of the more recent tools and approaches including them in a single project framework (the IUCN cycle used for nature reserve planning), spanning all from the analysis of the context (both in project teams and in real world), to the planning stage until the monitoring phase. We encourage practitioners to use these innovative tools and approaches in their projects that are focused on problematic wildlife.