Despite the academy's commitment to the idea of meritocratic and fair principles in recruitments, promotions, student admissions and progress, gender segregation and gender inequalities continue to trouble universities worldwide. Through case-studies of two education programs at a Swedish university, we investigate how processes of formal merit, both formal (required for admission such as high grades) and what we identify as informal merit (needing to act in particular ways once admitted) work to obviate or reproduce gender-segregation. We analyze how everyday gendering processes in the classroom play a central role in what gets constructed as merit. Changing notions of merit during the period of study can hamper possibilities for ending gender segregation in HE or open up for ways to circumvent it. We show that a complex and ongoing construction of informal merit can restrain students from minority groups (in relation to gender, but also ethnic background, socioeconomic position, or sexuality) to enter, and importantly, remain in the program. At the same time, new ways of addressing the subject itself provides potential openings. We argue that in order to achieve gender balance at universities, it is urgent to understand how informal and formal merit interplay once students have joined the university and importantly also when they have made the leap and broken with gender segregated education choices.