Ecosystems are subjected to increasing exposure to multiple anthropogenic drivers. This has led to the development of national and international accounting systems describing the condition of ecosystems, often based on few, highly aggregated indicators. Such accounting systems would benefit from a stronger theoretical and empirical underpinning of ecosystem dynamics. Operational tools for ecosystem management require understanding of natural ecosystem dynamics, consideration of uncertainty at all levels, means for quantifying driver-response relationships behind observed and anticipated future trajectories of change, and an efficient and transparent synthesis to inform knowledge-driven decision processes. There is hence a gap between highly aggregated indicator-based accounting tools and the need for explicit understanding and assessment of the links between multiple drivers and ecosystem condition as a foundation for informed and adaptive ecosystem management. We describe here an approach termed PAEC (Panel-based Assessment of Ecosystem Condition) for combining quantitative and qualitative elements of evidence and uncertainties into an integrated assessment of ecosystem condition at spatial scales relevant to management and monitoring. The PAEC protocol is founded on explicit predictions, termed phenomena, of how components of ecosystem structure and functions are changing as a result of acting drivers. The protocol tests these predictions with observations and combines these tests to assess the change in the condition of the ecosystem as a whole. PAEC includes explicit, quantitative or qualitative, assessments of uncertainty at different levels and integrates these in the final assessment. As proofs-of-concept we summarize the application of the PAEC protocol to a marine and a terrestrial ecosystem in Norway.