Background. Drawing on social identity theory and positive psychology, this study investigated women’s responses to the social environment of physics classrooms. It also investigated STEM identity and gender disparities on academic achievement and flourishing in an undergraduate introductory physics course for STEM majors. 160 undergraduate students enrolled in an introductory physics course were administered a baseline survey with self-report measures on course belonging, physics identification, flourishing, and demographics at the beginning of the course and a post-survey at the end of (...) the academic term. Students also completed force concept inventories and physics course grades were obtained from the registrar. Results. Women reported less course belonging and less physics identification than men. Physics identification and grades evidenced a longitudinal bidirectional relationship for all students (regardless of gender) such that when controlling for baseline physics knowledge: (a) students with higher physics identification were more likely to earn higher grades; and (b) students with higher grades evidenced more physics identification at the end of the term. Men scored higher on the force concept inventory than women, although no gender disparities emerged for course grades. For women, higher physics (versus lower) identification was associated with more positive changes in flourishing over the course of the term. High-identifying men showed the opposite pattern: negative change in flourishing was more strongly associated with high identifiers than low identifiers. Conclusions. Overall, this study underlines gender disparities in physics both in terms of belonging and physics knowledge. It suggests that strong STEM identity may be associated with academic performance and flourishing in undergraduate physics courses at the end of the term, particularly for women. A number of avenues for future research are discussed. (shrink)