Coastal ecosystems are complex and often support a broad spectrum of functions with competing objectives. In addition to their ecological value, they offer socio-economic benefits (i.e., ecosystem services) to coastal communities. One potential way to help address this complexity is to use decision support systems to help natural resources managers understand system dynamics and evaluate strategies to maintain the health and integrity of these ecosystems. This paper presents a roadmap and detailed application of co-production strategies where managers and researchers are fully engaged in a collaborative manner in the design of a decision support tool for coastal ecosystems. It also emphasizes the importance of capturing end-users’ (i.e., natural resource managers) priorities to refine the conceptual design of the decision support tool, while maintaining a sound scientific and modeling framework. The case study presented here centers on the Northern Gulf of Mexico, but the concept can be exported globally to other systems. This effort highlights foundational co-production strategies, including transdisciplinary team assembly, a knowledge sharing workshop, Toolbox Dialogue Initiative workshops to facilitate working across disciplines, core team and focus group meetings, and design charrettes. Further, this paper articulates the benefits and difficulties of executing a co-production process through virtual collaborations.