The report summarises the main conversations at and around the workshop "Empowering civil society through participatory investigation?". The event was dedicated to exploring new types of interactions between science and society, which we called participatory investigation, and how such interactions can contribute to the empowerment of civil society. We wanted to discuss such interactions from the perspective of civil society organisations (NGOs), a point of view that has so far been largely neglected, at least in the European citizen science community. The workshop was organised in collaboration by European Citizen Science Association (ECSA), especially the H2020 project Doing it Together Science (DITOs), Pour une alliance sciences en société (ALLISS), Institut francilien recherche, innovation, société (IFRIS), Laboratoire Interdisciplinaire Sciences Innovations Sociétés (LISIS) and the Living Knowledge Network (LKN).