This article aims to evaluate the effect of the COVID-19 pandemic on malnutrition among children under two years of age enrolled in the Bolsa Família Program (BFP). Ecological study of interrupted time series (ITS), with low weight for age, stunting, and overweight as time-dependent variables of malnutrition, extracted monthly (Jan/2008 to June/2021) from the Food and Nutrition Surveillance System. The COVID-19 pandemic was the exposure, dichotomized into pre-pandemic and pandemic. In RStudio, the trend was obtained by Prais-Winsten regression, and the effect of the pandemic on the time-dependent variables was determined by SARIMA modeling, estimating the regression coefficients (RC) adjusted for trend and seasonality (α = 5%). The pandemic was associated with an increase in: i) low weight for age in the South (RC = 0.94; p < 0.001) and Southeast (RC = 1.97; p < 0.001); ii) height deficit in the Midwest (RC = 2.4; p = 0.01), South (RC = 2.15; p < 0.001) and Southeast (RC = 2.96; p < 0.001); and iii) and overweight in the North (RC = 1.51; p = 0.04), Midwest (RC = 2.29; p = 0.01), South (RC = 2.83; p < 0.001), and Southeast (RC = 0.72; p = 0.04). The pandemic increased underweight in the South and Southeast, and the double burden of malnutrition in the Midwest, South, and Southeast. In the Northeast and North, higher rates of malnutrition still persist.