Ph.D. training across academic disciplines has faced significant challenges, with news and media outlets regularly highlighting student struggles, including frequent distrust and antagonism in relationships with faculty advisors. Given the centrality of the advisor–advisee relationship in doctoral education—most programs follow an apprenticeship model where students are mentored closely by a primary faculty advisor—the quality of this relationship may be particularly important. Yet almost no empirical research has systematically examined the long-term implications of advisor trust in doctoral education. In a prospective longitudinal study of 558 incoming Ph.D. students—primarily in STEM (Science, Technology, Engineering, and Mathematics) fields—at three US research universities, we examined the role of Ph.D. students’ trust in their advisor early in graduate school on 17 outcomes measured repeatedly during students’ first year, a sensitive period when a disproportionate number of students have historically exited. Results revealed a surprisingly broad and consistent effect of advisor trust, such that students who had greater trust in their advisor finished their first year more motivated, higher in well-being, and more academically successful than those with lower advisor trust. These effects were independent of student and advisor demographics, students’ academic preparation, individual characteristics, and existing differences in outcomes measured at the start of graduate school, highlighting the potential causal implications of advisor trust for shaping a successful and healthy Ph.D. journey.