Training researchers represents a substantially deeply international activity for higher education, and yet the transition into independence, a critical aim of doctoral education, remains a challenge for both supervisors and doctoral students, especially those from different cultural backgrounds. Interactions between Chinese doctoral students and their supervisors at Dutch universities exemplify the challenges in such an intercultural context. Interviews with 21 Chinese doctoral students and 16 supervisors from three Dutch universities reveal three potential challenges to fostering independence: (1) misalignment in supervisors' and students' conceptualizations of independence due to implicit diversity; (2) misalignment between supervisory support and students' zone of proximal development (ZPD) of independence, as derived from the broader ZPD concept, especially in the first year of the doctoral study; and (3) a gap between supervisors' interpretation of students' visible learning behavior and students' actual concerns. We provide a rich description of these hidden challenges and conclude with a framework outlining the relationships among the three layers of challenges. In so doing, we provide detailed information and a practical tool for supervisors to increase students' awareness and skills, accurately diagnose students' ZPD, recognize and reduce any potential misalignments in time, and thereby support students' transition into independence. We conclude by discussing the practical and theoretical implications of our findings for supervisors and students in other intercultural contexts to reflect on their own practices and explore new ways of promoting international students' transition into independence.