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Undergraduates may face challenges to assure food security, related to economic and mental distress, especially during the COVID-19 pandemic. This study aimed to assess food insecurity and its associated factors in undergraduates during the COVID-19 pandemic. An online cross-sectional study was conducted from August 2020 to February 2021 with 4775 undergraduates from all Brazilian regions. The questionnaire contained socio-economic variables, the validated Brazilian food insecurity scale, and the ESQUADA scale to assess diet quality. The median age of the students was 22.0 years, and 48.0% reported income decreasing with the pandemic. Food insecurity was present in 38.6% of the students, 4.5% with severe food insecurity and 7.7% moderate. Logistic regressions showed students with brown and black skin color/race presented the highest OR for food insecurity; both income and weight increase or reduction during the pandemic was also associated with a higher OR for food insecurity, and better diet quality was associated with decreased OR for food insecurity. Our study showed a considerable presence of food insecurity in undergraduates. Policy for this population must be directed to the most vulnerable: those with brown and black skin color/race, who changed income during the pandemic, and those presented with difficulties maintaining weight and with poor diet quality.