Climate change could irreversibly alter Southern Ocean ecosystems. Marine ecosystem model (MEM) ensembles can help policymakers by projecting future changes and assessing management approaches. However, projections from the Fisheries and Marine Ecosystem Model Intercomparison Project (FishMIP) global MEM ensemble reveal an uncertain future for the Southern Ocean, indicating a need for a region-specific ensemble. Significant model uncertainty arises from the Earth system models (ESMs) used to drive FishMIP models, particularly regarding future changes to lower trophic level biomass and sea-ice coverage. To enhance confidence in regional MEMs as tools for ecosystem-based management in a changing climate, we propose developing a Southern Ocean Marine Ecosystem Model Ensemble (SOMEME) as part of the FishMIP 2.0 regional model intercomparison initiative. A key challenge is balancing global standardized inputs with regional relevance. As a first step, we design a SOMEME simulation protocol that builds on and extends the FishMIP framework. This includes: detailed skill assessment of climate forcing variables for Southern Ocean regions, extending fishing data to include whaling, and new simulations assessing ecological links to sea-ice processes in an ensemble of candidate regional MEMs. These efforts will improve assessments of climate change impacts on Southern Ocean ecosystems.