Although instructional designers are experienced and positioned to be leaders in online learning, it was not previously known how organizational structures influenced their ability to act as leaders in their institutions. This problem warranted a deep exploration of the organizational structures for instructional design teams in higher education. This qualitative, multi-case study consisted of three individual universities each with a different organizational structure profile. Data were collected through semi-structured interviews and document analysis with participants in three key roles at each institution: dedicated instructional designer, online faculty member, and online learning administrator. The research culminated in within-case analyses of each institution and a comparative case analysis of all three studied institutions. The results of the study revealed that the organizational structure that most positively influenced instructional design leadership was a centralized instructional design team with academic reporting lines. Decentralized instructional designers experienced significant disempowerment, role misperception, and challenges in advocacy and leadership, while instructional designers with administrative reporting lines experienced a high level of role misperception specifically related to technology support. Positional parity between dedicated instructional designers and faculty, in conjunction with implementation of the recommended organizational structure, was found to be critical to empowering designers to be partners and leaders.