Several international legal agreements and guidelines have set the minimum standards and key principles to guide the implementation of an ecosystem approach for the management and conservation of highly migratory fish species. Since its creation IOTC has had the ability to assimilate some of these principles in the form of adoption of formal management measures. Yet these management measures have not provided practical guidance on how to make operational an Ecosystem Approach to Fisheries Management (EAFM) within its convention area. The Specific Contract N0 2 “selecting ecosystem indicators for fisheries targeting highly migratory species-” under the Framework Contract - EASME/EMFF/2016/008 provisions of Scientific Advice for Fisheries Beyond EU Waters- addresses some scientific impediments and provides solutions that shall support the implementation of an EAFM in IOTC. Here, we present some preliminary results of this project with the objective of seeking collaboration and broad consultation with IOTC. First, we summarize properties of success from other regions of the world in operationalizing the ecosystem approach which could be transferred to IOTC. Second, we provide a list of candidate ecosystem indicators to monitor the broader impacts of IOTC fisheries on the pelagic ecosystem. Third, we propose two potential ecoregions within the Indian Ocean which could be used to guide region-based ecosystem plans, assessments and research. Fourth, we present the key elements of a pilot ecosystem plan to be developed for one case study region. Ultimately, the products created throughout this study aim to facilitate the linkage between ecosystem science and fisheries management as well as facilitate the process to operationalize an EAFM in IOTC.