The number of women studying STEM careers and pursuing graduate degrees has not changed in the last decade (National Student Clearinghouse Research Center, 2015; Science & Engineering Degree Attainment: 2004–2014). Most prior research to explain this problem has focused on the topics of identity, access, pedagogy, and choice (Brotman & Moore, 2008; Journal of Research in Science Teaching, 45, 971–1002). Additional research is needed on how internal and external factors interact with one another to demotivate girls and young women from pursuing science careers. Here, we show how girls’ competency beliefs are an essential foundation for science content learning during middle school and how these effects of competency beliefs are mediated by in and out‐of‐school factors. We recruited over 2,900 6th and 8th grade students from two different regions in the United States. At two different time points, students completed surveys asking about their stance toward science such as competency beliefs in science, willingness to engage in argumentation, and choice preferences toward optional science experiences. We also collected a reasoning ability measure, and pre‐ and post‐tests on science content knowledge. Moreover, students also reported on their cognitive behavioral engagement during a sampled science class on two separate occasions. Multiple regression and mediation analyses show that as boys grow older, their willingness to engage in argumentation and to participate in science experiences suppresses the role of competency beliefs on their learning science content. By contrast, as girls grew older, they showed an increasing need to have high competency beliefs to achieve strong content learning gains. Our results demonstrate that despite girls’ willingness to participate in scientific argumentation and to take part in science experiences, they probably do not receive enough support in their environment to access the benefits of these experiences, and hence they have a stronger need to have high competency beliefs in order to achieve significant growth in science learning. © 2017 Wiley Periodicals, Inc. J Res Sci Teach 54:790–822, 2017