Objective: To compare rates of anxiety and depression among LGBTQ college students before and during the COVID-19 pandemic and examine pandemic-related stressors and protective factors. Participants: Two cohorts of LGBTQ college students, aged 18-25, sampled before (N = 3,484) and during (N = 1,647) the pandemic. Methods: The Healthy Minds Study (HMS) is an annual mental health survey administered to college students in the United States, which included additional items related to the COVID-19 pandemic. Results: Mean anxiety symptoms were significantly lower mid-pandemic compared to pre-pandemic, but no differences in mean depressive symptoms were detected. Results varied by sexual and gender minority status. Financial stress, pandemic-related concerns, and witnessing discrimination were risk factors while academic persistence, positive mental health, and formal support were protective factors. Conclusions: Mental health and instrumental support from institutions will be critical for college students during the pandemic. Affirming and empowering spaces for LGBTQ college students may leverage protective factors.