A growing number of global ocean conflict studies over the last decade have set out to advance sustainability in the Anthropocene. Many of these research projects use multiple case studies to extract lessons for wider contexts. The methods used by these studies, and the extent to which their results have validity beyond the individual case study, often remain unclear. This paper explores the challenges in performing cross-case analysis within what we denote as case-based globally focussed sustainability projects (CB-GSPs) and indicates solutions by combining information from semi-structured interviews with leading scientists from eight CB-GSPs. We identify six distinct challenges that are common across these studies with regard to generating actionable knowledge through cross-case analysis. Based on these findings, we propose a set of best practice recommendations for scientists, project partners, and funders to co-produce actionable knowledge for global projects on ocean conflict.