The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has affected millions of people around the world. In Colombia, 1.65 million cases and 43,495 deaths were reported in 2020. The exacerbation of poverty is a critical consequence of the pandemic, particularly in low- and middle-income countries. Schools have been closed in many places around the world to slow down the spread of SARS-CoV-2 and particularly in Latin America. In Bogotá, Colombia, public schools were closed since March 2020 and stayed closed for in-person instruction for the rest of the year, except for some schools that were open as a pilot for testing policies. To reconcile these two priorities in health and poverty, we estimated the impact of school reopening for in-person instruction in 2021. We used an agent-based model of SARS-CoV-2 transmission, considering social contact. The model includes schools that represent the set of private and public schools in terms of age, enrollment, location, and size. The model is calibrated to daily incidence of deaths in Bogotá. We simulated school reopening at different capacities, assuming high use of face mask, and evaluated the impact on the number of deaths in the city of different scenarios of school reopening by grade, and multidimensional poverty index. We found that school reopening, based on a correct use of face masks at 75% in >8 years of age, at 35% capacity had a small impact on the number of deaths reported in the city, assuming that overall mobility in the city was similar to the mobility during November. The increase in deaths was smallest when only pre-kinder was opened, and largest when secondary school was opened. Even at larger capacities, the impact on the number of deaths of opening pre-kinder was below 10%. Reopening other grades above 50% of capacity could significantly increase the number of deaths in the city. Reopening schools based on the multidimensional poverty index resulted in a similar increase in the number of deaths, independently on the level of poverty of schools. We conclude that the impact of schools reopening for in-person instruction is lower for pre-kinder grades and the magnitude of additional deaths associated with school reopening can be minimized by adjusting capacity in older grades. In addition, opening lower grades could allow adults, especially the poorest women to return to work.