As Natura 2000 missed challenges of halting biodiversity decline, its’ management is being affected by factors of ecological, political, and economic character. To address the shortcomings revealed during the Fitness Check and to facilitate meeting the EU’s biodiversity targets, the European Commission developed an “Action Plan for Nature, People and the Economy” prioritizing areas for improvement. However, mixed views still exist on the Natura 2000 governance; it is not certain that Action Plan would address existing drawbacks. The aim of the research was to identify divergent and convergent experts’ attitudes towards biodiversity conservation in Europe, with a focus on forward-looking environmental governance and policy-informing perspective. Participants representing multiple disciplines and professional backgrounds related to planning, governance, or management of Natura 2000 sites provided a comprehensive overview on the topic and address-related challenges. Based on the results of a Delphi survey, we established a framework for illuminating the spaces of disjunction in experts’ views towards Natura 2000 conservation. We distinguished three main divergence areas in views towards future network operation: (1) raising public awareness of environmental problems in the network, (2) the role of the European Commission in building political ownership of Natura 2000 sites among landholders, and (3) funding of Natura 2000. Then, based on revealed dichotomies, we return with drawing a roadmap for promoting more consensual outcomes. The results should help enable the practical management of conflicting views and the effective engagement of future biodiversity conservation strategies in Europe and beyond.