In chemistry, lack of academic preparation and math ability have been offered as explanations as to why women seem to enroll, perform, and graduate at lower levels than men. In this paper, we explore the alternative possibility that the gender gap in chemistry instead originates from differential gender effects of academic factors on students’ motivation. Using a sample of approximately 670 students enrolled in a mid-sized university in the United States we conducted: (1)t-tests to understand incoming academic differences between freshman students by gender, (2) regression analysis to determine which academic and attitudinal factors predict success in General Chemistry 1, and (3) a mediation analysis to understand the underlying mechanisms of how academic performance affects students’ beliefs about their competency in chemistry, which in turn has an effect on chemistry achievement. We demonstrate the importance of math ability as a contributor to chemistry achievement, but further that ability differences in math are important because they affect students’ chemistry competency beliefs. Critically, this link between ability and competency beliefs is stronger for women than men. These results suggest that interventions geared towards improving women's chemistry competency beliefs could have an important influence in improving their achievement in the classroom, and in consequence reduce the gender gap in chemistry.