This article focuses on the topic of gender segregation at universities in German-speaking countries. It addresses the question how the interrelation of organizational structures and individual biographies leads to the drop-out of females during their PhD. Moreover, it contributes to the understanding of how these drop-outs are embedded in gendered organizational structures and processes. A case study approach is applied in order to gain a deeper understanding of the crucial mentor–mentee relationship at this career stage. The detailed reconstruction of narrative biographies shows how a young female researcher faces too many restrictions and too much freedom at the same time. Results revealed how the female junior is highly dependent on the male senior and that specific assignments of how and with whom to work impact her career development. At the same time, the evaluation of the junior’s work is based on the stereotypical picture of an autonomous scientist who produces excellent research results without senior interference. Findings are explained in line with the theory of trajectory curves, and demonstrate the long-term and complex process of the unplanned drop-out of a female researcher in a male-dominated environment with gendered structures and processes.