Research has shown that achieving gender equality in science goes beyond equal gender ratios in the classroom. Female students in science disciplines with relatively higher female participation rates (e.g. biology and chemistry) still experience similar gender issues as students in male-dominated science disciplines (e.g. physics and mathematics). Yet, when studying gender inequality in science, these so-called ‘gender-balanced’ disciplines are frequently ignored. This study aimed to investigate gender issues for students in biology and chemistry and explore how these experiences were impacting their persistence in the science, technology, engineering, and mathematics (STEM) educational and career pipeline. Findings showed that both male and female students commonly believed that issues of gender were restricted to the male-dominated science disciplines. However, female students still reported experiences of gender bias, commonly through the form of implicit discrimination. The importance of the affective domains was also highlighted, with science identity and belonging impacting the female student experience and their intentions to persist in the sciences. Results from this study suggest further work is needed in ‘gender-balanced’ science disciplines, specifically in the emotional domains of science identity and belonging. This research may help educators develop more effective intervention programmes for increasing women’s persistence in the STEM pipeline.