Between 2014 and 2016, an interdisciplinary team of researchers including physical oceanographers, biologists, economists and anthropologists developed a working example of an Integrated Ecosystem Assessment (IEA) for three ecologically distinct regions of the Northwest Atlantic; Georges Bank, the Gulf of Maine and the Grand Banks, as part of the International Council for the Exploration of the Sea (ICES) Working Group on the Northwest Atlantic Regional Sea (WGNARS). In this paper, we review the transdisciplinary and collaborative process by which the IEA was developed, with a particular focus on the decision points arising from the IEA construct itself. The aim is to identify key issues faced in developing any IEA, practical decisions made to address these issues within the working group and lessons learned from the process.