This paper examines the structure of scientific collaborations in Berlin as a specific case with a unique history of division and reunification. It aims to identify strategic organizational coalitions in a context with high sectoral diversity. We use publications data with at least one organization located in Berlin from 1996–2017 and their collaborators worldwide. We further investigate four members of the Berlin University Alliance (BUA), as a formerly established coalition in the region, through their self-represented research profiles compared with empirical results. Using a bipartite network modeling framework, we move beyond the uncontested trend towards team science and increasing internationalization. Our results show that BUA members shape the structure of scientific collaborations in the region. However, they are not collaborating cohesively in all fields and there are many smaller scientific actors involved in more internationalized collaborations in the region. Larger divides exist in some fields. Only Medical and Health Sciences have cohesive intraregional collaborations, which signals the success of the regional cooperation established in 2003. We explain possible underlying factors shaping the intraregional groupings and potential implications for regions worldwide. A major methodological contribution of this paper is evaluating the coverage and accuracy of different organization name disambiguation techniques.