The study analyzes relations between non-governmental organizations and public administration in Poland and the Czech Republic during the COVID-19 pandemic, with particular attention to the economic and institutional conditions of cooperation. The analysis is based on a qualitative comparative study using in-depth individual interviews conducted with representatives of non-governmental organizations in both countries. The collected empirical material was subjected to thematic analysis, combining deductive coding with the identification of emergent themes. The results indicate three key mechanisms: the paradox of flexibility in interpersonal relations alongside systemic rigidity; the replacement of co-governance with ad hoc crisis response; and a deepening asymmetry of resources and levels of professionalization between large and small non-governmental organizations. The adaptive capacities of organizations compensated for weak institutional support but did not lead to a lasting change in the model of cooperation. The article concludes with recommendations aimed at strengthening co-governance mechanisms and ensuring stable funding for non-governmental organizations.