Governments increasingly apply collaborative governance based on deliberation that typically takes place in non-majoritarian institutions. However, collaborative institutions face accountability challenges depending on their institutional design. Still, empirical research is missing on the different choices member states make when designing collaborative institutions implementing European Union (EU) political goals. Using four theoretical principles of accountability, the study compares how Finland and Sweden implement the requirements for collaborative governance of two EU directives in national legislation and management plans. While Finland has provided more detailed and stricter rules resulting in higher process accountability, Sweden has delegated final decision making to authorities, achieving a higher degree of institutional independence. The results reveal that since the directives set only some of the key rules and procedures needed for achieving accountable collaborative institutions, member states’ discretion can lead to institutional variation even in similar governance contexts, resulting in differing institutional accountability and legitimacy of EU policies.