Despite various attempts to promote gender equity, the underrepresentation of women in STEM fields is still a major global issue with adverse implications for future economic and social development. Previous studies have identified that personal, institutional, and societal contexts influence equity, and the institutional level is critical in shaping women’s participation and achievements. Our study seeks to understand the gender differences in competency and challenge-based education in engineering programs. The research focused on the impact of institutional factors and personal characteristics of female engineering students on their strengthening of complex thinking. This is a transversal competency that allows all professionals to address and solve problems within their labor and personal spheres. We used a database with over 850,000 records containing the learning outcomes of engineering students (N = 16,524) enrolled at a Mexican private university between 2019 and 2022. After cleaning and balancing for gender and assessment of the competency (observed or not), we worked with 56,569 records from 5711 students. Through logistic regression models with 5-fold cross-testing on 10 features and their interpretation through Shapley values, we identified the institutional factors that contribute to the strengthening of the complex thinking competency of female undergraduates in engineering programs. This work contributes to understand the challenges faced by female students in STEM education and provide practical solutions for promoting gender equity within the learning environment. In addition, the findings will assist higher education institutions in improving future education to increase women’s representation in STEM and contribute to better and equitable societies.