Background: The COVID-19 pandemic has considerably increased food insecurity with disproportionate social and racial distribution. The present study aimed to examine the persistence of food insecurity and the associated factors during the pandemic. Methods: A cohort study was conducted in two São Paulo city slum, Brazil. Participants answered questionnaires in three moments: April and October 2020 and April 2021. Food insecurity was assessed using the Brazilian food insecurity scale (EBIA) comprising five questions. Temporal trends in sociodemographic, economic, social assistance coverage, food insecurity, and difficulties related to buying personal use goods were assessed using the Kruskal-Wallis or x2 test. Prevalence ratios of food insecurity persistence categorized as “never,” “sometimes in food insecurity,” “always in food insecurity,” were calculated using the Poisson regression model. Results: A total of 424 householders completed two assessments. The majority of householders were young, non-White women; more than half of householders had less than nine years of education and were working in non-qualification jobs. During the follow-up, families covered by social assistance increased; however, their income had decreased (p<0·05). From 302 householders that completed three assessments, 33% were “always in food insecurity”, and 46% were “sometimes in food insecurity”. Low income in the second wave was associated with “always in food insecurity” [aPR=1·62 (95%CI: 1·17-2·24)], regardless of education level. Households constantly facing difficulties related to buying gas canisters [aPR=2·54 (95%CI: 1·78-3·62)], hand sanitizers [aPR=5·67 (95%CI: 83·24-9·91)], and basic hygiene products [aPR=4·08 (95%CI: 2·49-6·68)] were associated with “always in food insecurity” independent of education. Conclusions: The COVID-19 pandemic has adversely impacted the key factors of health maintenance. Guarantees of sufficient food quantities and regularity, and without risk of losing access to basic needs, must be guaranteed by the cross-government action to fight social inequities.