The current study aimed to examine the advisor-advisee relationship from the perspectives of both advisees and advisors throughout the doctoral education process, deciphering the internal mechanisms of universities related to doctoral advisement and the role of the advisor-advisee relationship in the development of future scientists. A qualitative phenomenological research design was used through interviews conducted with 13 doctoral students and 18 faculty members at two high-ranking public research universities with well-established advisor-advisee processes and strong organizational cultures. The results demonstrate the expectations of both parties from each other and themselves throughout the process as well as the effects of the advisor-advisee relationship on the efficiency of the process, advisees’ future academic careers, and identities. Advisees generally focused on communication and planning thesis work with advisors while the advisors stressed how different dimensions of the supervising process affect the understanding of scientist identity. Additionally, it was concluded that students feel closer to being a scientist/researcher when they feel the support of their advisor and have a close relationship with their advisor, and the discourses of advisors extend this argument to feeling the support of all faculty members as a team. The study highlights the important role of advisors in raising future scientists which demonstrates the need for universities to find ways to support faculty members in developing their supervisory skills.