Established under the European Union (EU) Birds and Habitats Directives, the thirty-year transnational Natura 2000 network is considered a fundamental biodiversity conservation framework worldwide. The global financial crisis has afflicted European economies since 2008 and has not only caused radical changes to the economic development, but has also resulted in major implications on nature conservation activities in one of the weakest EU member states, Greece. With a strong tradition in managing its high nature value in a centralized and questionable way, in the face of the economic crisis, implementation challenges of the Greek state concerning Natura 2000 have been enlarged. This research constitutes a broad-based assessment of the effects of the current economic crisis on the application of the EU Birds and Habitats Directives by the Greek state. By using an expert-based participatory approach (the Delphi technique) we attempt to address the impact of the crisis on the administrative levels, competent authorities and procedural frames of the national protected area system, as perceived by key stakeholders and experts. The Delphi approach allowed a systematic collection of experts’ transdisciplinary judgements on the state of the Greek Natura 2000 network in terms of implementation, management, administration, monitoring and legislation. According to the substantial part of the Greek conservation community that participated in the survey, many enforcement obstacles are a product of either direct or indirect consequences of the economic crisis, while some are inherent to the lack of a national comprehensive conservation strategy. This study involved also an evaluation of the practices and obligations of the responsible management authorities of the Greek protected areas to get an insight of the “on the ground” financial consequences on their operation. Based on our findings we propose recommendations for improvements and measures that can substantially counteract the negative impacts of the economic austerity on the enforcement of nature conservation.