Facing intense global competition and pressure from public authorities, several universities in Europe have engaged in merger and concentration processes. Drawing on two in-depth case studies, this paper considers university mergers as an opportunity to explore the processes involved in the creation of a new organizational structure. In line with recent scholarly calls to revisit the notion of organizational design, we combine insights from three different research streams to address the functional, political, and institutional dynamics that shaped the organizational architecture of the merged universities. Two main results are presented and discussed. First, although these mergers were initiated largely in response to the diffusion of new global institutional scripts, these scripts had little influence on organizational design: deeply institutionalized local scripts prevailed over global mimetic pressures. Second, while these institutional scripts provided many of the basic building blocks of the new universities, in both cases their design was also heavily shaped by time pressures and power games. While a few powerful actors used the merger as an opportunity to promote their own reform agenda, some of the key features of the two merged universities stemmed from choices by exclusion, whose primary aim was the avoidance of conflicts.