This study employed a critical inquiry paradigm to explore the significance of equity and social justice in teaching qualitative methodologies and methods to graduate students. Graduate students of multiple minoritized identities and a faculty member conducted a two-year inquiry into the research apprenticeship experience, including the stages of student-led conceptualization, data collection, analysis, international conference presentation, and publication. The study investigated the experiences of the faculty and students as well as the responsibilities of the institution against the backdrop of historical and contemporary pandemics. Consequently, we problematized hidden curriculum and unconscious assumptions to suggest research course design sequencing improvements. The findings emphasize the impact of these experiences on qualitative research teaching and learning practices and institutional responsibility to graduate student research apprenticeships. The Graduate Research Apprenticeship Nested Design Pathway is presented as a tool that institutions worldwide can adapt and implement to serve the complex needs of their students.