National lockdowns and containment measures to control the spread of COVID-19 led to increased unemployment, lower household incomes and reduced access to affordable and nutritious foods globally. This study aimed to examine changes and correlates of household food insecurity experience and mitigation strategies adopted in peri-urban Peru during the COVID-19 pandemic. Low income households with children age < 2 years in Lima and Huánuco participated in three repeated cross-sectional surveys from 2020 to 2022 (n = 759). We assessed changes in household food insecurity experience using the Food Insecurity Experience Scale. Correlates of moderate-severe food insecurity were analysed using univariate and multivariable linear mixed-effect regressions. We also assessed perceived impacts of the pandemic on livelihoods, coping strategies and receipt of financial or food assistance. Moderate-severe food insecurity was 47.0% in 2020 (survey 1) decreasing to 31.1% in 2022 (survey 3). In adjusted analyses, food insecurity was higher in households with perceived reduced income (β = 12.69 [6.82; 18.56]); in the lower socio-economic status (SES) tertiles ( compared to the relatively highest SES tertile ; middle tertile (β = 20.91 [9.89; 31.93]), lowest tertile (β = 39.37 [28.35; 50.40]); in households with ≥ 2 children < 5 years (β = 8.78 [2.05; 15.50]); and in Lima ( compared to Huánuco ; β = 10.47 [1.27; 19.67]). Food insecurity improved more among the relatively lowest SES compared to the relatively highest SES households between survey 1 and 3 (interaction p = 0.007 ). In conclusion, almost half of households experienced moderate-severe food insecurity mid-pandemic with greater risk observed in the most socio-economically disadvantaged households. The inequality gap in food insecurity associated with SES narrowed over time likely due to household coping strategies and reduced poverty.