The rise of transnational nonstate certification programs has contributed to complex accountability relations surrounding efforts to hold companies accountable for their environmental and social impacts. We examine how decisions about goals, engagement of stakeholders, and accountability mechanisms in the Marine Stewardship Council (MSC)—a fisheries certification program—have affected the controversies facing the program and how it has sought to address them. We reveal a misalignment between environmental groups and the MSC. Both seek to advance sustainable fisheries, and the market campaigns of environmental groups have supported certification. However, the MSC has provided these groups limited influence over its governance; it has responded to external demands for accountability by focusing on internal accountability, and reforming its assessment and objection procedures. Environmental groups have responded by working to decouple their market and information campaigns from supporting the MSC. These outside strategies demonstrate that a private voluntary program’s execution of institutional accountability mechanisms (tier-two accountability) is significantly affected by the critical judgements of outside audiences about whether the program has been set up to address the right problem framing and goals (tier-one accountability).