The intensive harvest of wild populations for food can pose a risk to food security and to conservation goals. While ecosystem approaches to management offer a potential means to balance those risks, they require a method of assessment that is commensurate across multiple objectives. A major challenge is conducting these assessments in a way that considers the priorities and knowledge of stakeholders. In this study, we co-developed an ecological risk assessment (ERA) for fisheries in California (USA) with scientists, managers, and stakeholders. This ERA was intended to meet the requirements of existing policy mandates in the state of California and provide a systematic, efficient, and transparent approach to prioritize fisheries for additional management actions, including the development of fisheries management plans fully compliant with California laws. We assessed the relative risk posed to target species, bycatch, and habitats from nine state-managed fisheries and found risk to target species was not necessarily similar to risks to bycatch and habitat groups. In addition, no single fishery consistently presented the greatest risk for all bycatch or habitat groups. However, considered in combination, the greatest risk for target species, bycatch groups, and habitats emerged from two commercial fisheries for California halibut. The participatory process used to generate these results offers the potential to increase stakeholders' trust in the assessment and therefore its application in management. We suggest that adopting similar processes in other management contexts and jurisdictions will advance progress toward ecosystem-based fisheries management that simultaneously satisfies fisheries, conservation, and relationship-building objectives.