We investigated how the endorsement of gender stereotypes affects disciplinary identity across three different science-technology-engineering-mathematics (STEM) areas: physics, biology, and chemistry, and whether such relationship is mediated by self-concept constructs, such as self-efficacy and perceived academic control. Building on the ambivalent sexism theory and masculine ideology paradigm, we focused on gender stereotypes based on hostile and benevolent sexism and on male role norms. A sample of 1406 Italian high school students (girls = 742) was involved in the study. Structural equation modeling was used to test the hypothesized relationships. Results show that the adherence to male role norms and the rejection of hostile sexism have a significant effect on the development of a disciplinary identity in the three targeted STEM domains. However, such an effect is fully mediated by self-efficacy and perceived academic control. Moreover, the identity in the three addressed STEM domains is differently affected by the endorsement of stereotypes, with physics and biology being more largely affected than chemistry. More importantly, the endorsement of hostile sexism stereotypes significantly decreases the perceived self-efficacy, while higher levels of perceived academic control are predicted by higher levels of endorsement of male role norms, for both girls and boys. Our findings suggest that to reduce the perception of femininity as incongruent with STEM identification, it would be necessary to deconstruct the masculine view of self-efficacy and academic control.