Abstract Small pelagic fisheries management is difficult because they exhibit large natural abundance fluctuations and are considered forage fish. We discuss the challenges faced by these fisheries within the Marine Stewardship Council (MSC) sustainability certification framework, which evaluates the sustainability of fish stocks, the environmental impact, and effective fisheries management. Certification suspension is frequently linked to the sustainability of stocks. For MSC certification, scientific research will need to play a major role in filling key knowledge gaps, particularly on the nature and causes of ecosystem productivity changes (including climate change), and the role of small pelagics in the ecosystem. Different from other cases where MSC certification creates a direct market incentive through price premiums, in these fisheries, the incentive is related to fisher's public image and improves the bases for negotiation with authorities and the conservation sector. In this context, strategic cooperation between fisheries under the certification process may provide them more benefits than competition.