Many geoscience education initiatives now involve cross-departmental or multi-institutional programs. However, the geoscientists who lead such programs typically have little experience or training in program design, leadership, or evaluation. In this commentary, we make the case that geoscientists taking on these ambitious leadership roles can draw on a set of understandings and skills that they already have: the tools and habits of mind of systems thinking. Using examples from the InTeGrate program, we suggest ways to envision, shape, and monitor an educational intervention by thinking of oneself as building and improving a complex system with constituent subsystems. Suggestions for the design phase include the following: Decide on an essential suite of subsystems and plan for them to interact in mutually beneficial ways. Consider using a set of semi-autonomous parallel subsystems that will allow for replication with adaptation as experience accrues. Plan for nonlinear causality chains in which one activity has multiple beneficial outputs, and desired outcomes are supported through multiple influencers. At the implementation phase, leverage feedback loops to nudge actors toward desired behaviors and away from problematic choices. Build technical and social mechanisms to regulate flows of information between and within subsystems, so as to deliver timely, actionable information without overloading the actors. In evaluation, use systems mapping to understand where critical dependencies occur and insert evaluative probes at these locations. Seek out early indicators of emergent phenomena and conceptualize long-term outcomes in terms of modifications to the larger system of higher education.