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Prior literature has documented the importance of faculty advisors in the doctoral student socialization process, with a few studies describing negative advising relationships characterized by disengagement, disinterest, unsupportive behavior, and interpersonal conflict. We extend this research by exploring how negative advising relationships emerge and develop over time. Examining longitudinal interviews over four years with 15 doctoral students in biological sciences in the USA who experienced negative relationships with their advisors, we illuminate how negative advising relationships unfold over the course of graduate studies. We find two primary patterns in challenging relationships: some students show a gradual decline in relationship health over time, while others point to a single event altering their relationship trajectory. We also identify specific factors that shape each of these negative relationship types. By revealing the different social processes that underlie the emergence of negative advising relationships, our findings provide a valuable contribution to understanding the complex social landscape of doctoral education. The findings further the dialogue on how faculty advisors can craft successful pathways through graduate education, thereby supporting the academic and professional success of doctoral students.