Previous studies have documented student-faculty interaction in STEM, but fewer studies have specifically studied negative forms of interaction such as discrimination from faculty. Using a sample of 562 STEM undergraduates from the National Longitudinal Survey of Freshmen, we use hierarchical generalized linear modeling to investigate various types of student-faculty interaction in Science, Technology, Engineering, and Math (STEM) and in particular, the link between discrimination from faculty and retention in STEM. While Black students interacted more frequently with faculty, they were also most likely to report experiencing racial/ethnic discrimination. Overall, female, Black, and Latinx students were more likely to leave STEM by the fourth year of college than male, White, and Asian American peers. Feeling that professors made a student feel uncomfortable due to race/ethnicity was negatively linked with STEM retention. None of the traditional forms of student-faculty interaction (i.e., non-discriminatory) predicted retention. Variation in patterns by race, gender, and income are discussed, as well as implications for research, policy, and practice.