This multi‐year, cross‐sectional qualitative study investigates gendered experiences of students and faculty at one master's degree‐granting military education institution in the United States. Findings from a grounded theory exploration into institutional climate using focus groups and classroom observations include themes of underrepresentation, tokenization, and dismissal during class conversations, and mischaracterization of diversity of thought. The studied institution responded to these findings by adopting a new gender‐blind class assignment process for students. The authors examined the resultant changes in the learning environment with regards to gender representation in classrooms that had zero, one, two, or three women. A next round of findings reflects students' conformance to gender norms, the prevalence of gatekeeping in class discussion, and the creation of affinity groups as a coping mechanism for underrepresented students. Findings also indicate the burden of intersectional representation falls disproportionately on women students; 73% of women students reflected two or more underrepresented‐group identities compared to just 7% of men students. Encompassing 114 h of classroom observations and 47 interviews with faculty and students, this research represents a rigorous and unprecedented cross‐sectional empirical inquiry into gendered experiences of a master's degree‐granting professional learning environment and has implications for scholars and practitioners working in male‐dominated organizations.