Cross-sector collaborative organizations are increasingly viewed as an effective means of addressing multifaceted health and social challenges. Given their dependence on volunteers to develop and implement strategy, members’ perceptions of future strategic priorities is a critical concern for leaders and sponsors of these organizations. Research set in more hierarchical, single-sector organizations acknowledges the important relationship between structure and strategy; however, relatively little research has explored these relationships in the context of collaborative organizations. We examined these relationships using multiple rounds of an Internet survey. All three dimensions of social structure (locus of decision making, formalization, and integration) had independent associations with participant’ perceptions of different strategic priorities, suggesting there is more than one approach to influencing the perceived priorities of the alliance. However, some dimensions of the social structure changed more than other dimensions over time, highlighting differential opportunities for influencing strategic priorities.