Indicator systems are seen as central tools for ecosystem-based fisheries management, helping to steer fisheries towards sustainability by providing timely and useful information to decision-makers. Without testing hypotheses about the links between policies and outcomes, however, indicator systems may do little more than promote ad hoc policies, possibly even prolonging the transition to sustainable fisheries. The Institutional Analysis and Development (IAD) framework is a robust framework that has been used extensively to design policy experiments and empirically test theories and models linking ecological–economic systems, institutions and the sustainability of common pool resource systems. A modified IAD framework is developed that transparently encompasses both process-oriented pressure-state-response (PSR) and structurally oriented sustainable livelihood indicator frameworks, thus providing a platform for ecosystem-based fisheries management policy experiment design and monitoring. An institutional approach to fisheries management facilitates critical examination of important cross-cutting issues, including assumptions regarding what comprises sustainability and how market, government and civil society organizations use strategic investments in capital assets and institutions to achieve sustainability objectives. The emphasis on capital assets keeps attention on the relative merits of alternative investment options in policy experiments.