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Abstract Working-class first-generation (FG) college students are underrepresented in higher education and STEM. Using a longitudinal quasi-experiment, we tested the impacts of a living learning community (LLC) in the biological sciences on FG students in their first year of college (Semester 1: N = 243; Semester 2: N = 199), across three cohorts (2018–2019, 2019–2020 and 2020–2021). Participation in the LLC enhanced FG students’ belonging, confidence, motivation, grades, knowledge of the social relevance of biology, and reduced STEM anxiety compared to a control group of FG students not in an LLC. LLC participation also increased retention in biological science majors one-year post-intervention compared to the control FG group. Moreover, LLC participation closed the academic gap between FG students in the LLC and honors students from college-educated families in a separate honors LLC. Benefits of the LLC intervention remained stable despite the COVID-19 pandemic, when living together became impossible, producing positive effects across cohorts from pre-pandemic to in-pandemic. Our results suggest that affinity-based learning communities—with or without shared housing—in the transition to college enhance academic thriving, persistence, and reduce social class driven achievement gaps in STEM.