Background: Race and gender disparities remain a challenge in science, technology, engineering, and mathematics (STEM) education. We introduce campus racial climate as a framework for conceptualizing the role of racial microaggressions (RMAs) as a contributing factor to the lack of representation of domestic students of color in STEM programs on college campuses. We analyze the experiences of students of color in STEM majors who have faced RMAs at the campus, academic, and peer levels. We draw from an online survey of more than 4800 students of color attending a large public university in the USA. The STEM major subsample is made up of 1688 students of color. The study estimates a series of Poisson regressions to examine whether one's race, gender, or class year can be used to predict the likelihood of the regular occurrence of microaggressions. We also use interview data to further understand the challenges faced by STEM students of color. Results: The quantitative and qualitative data suggest that RMAs are not isolated incidents but are ingrained in the campus culture, including interactions with STEM instructors and advisers and with peers. Students of color experience RMAs at all three levels, but Black students in the STEM majors are more likely to experience RMAs than other students of color in the sample. Conclusions: Our study demonstrates the need for campus officials, academic professionals, faculty members, and students to work together to address racism at the campus, academic, and peer levels. Additionally, STEM departments must address the impacts of the larger racial campus culture on their classrooms, as well as how departmental culture reinforces racial hostility in academic settings. Finally, our findings reveal the continued presence of anti-Black racism in higher education.