Anaerobic digestion (AD) plants undoubtedly represent an integral and irreplaceable element in rural energy transition and sustainable waste management. In our study, we focus on an advanced understanding of the dynamics behind the changing perceptions of AD plants in host communities in Poland, Slovakia, and the Czech Republic. The surveyed AD plant case studies were selected to represent best-practice examples of AD plant operations in their countries. By means of a comparative survey in three host communities, we seek to learn more about the shift in perceptions of AD plants between their planning and operational phases. We find that, although our cases are considered best-practice examples of AD plant operations, their overall support in their communities dramatically dropped in the operational phase consequent to real-life experience with living in the neighbourhood of an AD plant. Additionally, our findings indicate that respondents who reported the most severe deterioration of AD plant perceptions were, surprisingly, those who had participated in the planning process more than other respondents. The most frequently mentioned type of participation in the planning phase was reported to be visits to the local administration office to inspect an AD plant’s planning documentation. We argue that deteriorating perceptions of best-practice examples of AD plant operations negatively impact the further development and acceptance of the biogas sector in Eastern Europe. The element of acceptance by the locals of AD plant operations urgently requires reflection in the definition of best practices to inspire and upgrade both existing and planned biogas energy projects.