Nature-based tourism has become increasingly popular in recent years. However, the COVID-19 pandemic dramatically impacted the tourism sector and triggered contradictory processes, even in protected areas. This phenomenon opens up new opportunities for nature-based tourism from the perspective of rural development. In this study, we assess the relations between tourism and nature conservation and examine the characteristics of practical cooperation in three Hungarian national parks. Based on in-depth interviews (n = 76), document review, and analysis of tourism-related data, our research proves that nature-based tourism could play an essential role in rural development, but this is far from being fulfilled. None of the sectors have been able to impact the comprehensive development of the rural areas concerned. We conclude that sectoral partnership is inadequate, and there is no effective policy coordination. There is a lack of multiday tourism programs, and the currently available tourism infrastructure is insufficient. Initiatives such as the national park product trademark exist but are not well managed, so they do not have a meaningful impact. The results point out that cross-sector collaboration must be strengthened after the epidemic to provide a basis for policy coordination and joint planning.