In this methodological paper, I share methodological developments within an institutional ethnography (IE) guided by intersectionality. I argue both theories and methods that address how institutions operate through discourses of gender, race, and class inequity, which need to be used to guide interview research for pursuing equity in science, technology, engineering, and mathematics (STEM) education. Drawing on a political commitment to social justice foundational to intersectionality to guide the work, I detail methodological development for interview-based STEM social justice research. I describe how I developed interview methods on entry-level data by drawing on tools of storytelling, a post-interview reflection guide, and the Listening Guide. I reflect on how I adapted these tools for use in an IE to investigate the experiences of women who were parenting while pursuing STEMPhDs. Developing methods with theory was found to be generative for examining researcher and participant relationships, as was drawing on narrative approaches for greater examination of these relationships. Rather than presenting the work as settled, this paper grapples with the commitment and self-reflection needed in interpretative research with a social justice aim. Implications are shared for early career researchers and others who are interested in interview research for equity in STEM education.