Abstract Introduction According to OECD data, immigrant children were over-represented among COVID-19 cases compared to non-immigrant children. However, evidence is missing on whether their migrant status is associated with testing positive for COVID-19. Therefore, we aimed to estimate COVID-19 positivity rates among children residing in five municipalities of the Lisbon metropolitan area, Portugal, and to analyze migrant status as a determinant of health. Methods We conducted a prospective cross-sequential cohort study with 989 children born in 2015, 2018, and 2020 (48.5% non-immigrants; 51.5% immigrants). Sociodemographic data were collected through interview-based questionnaires, and the child’s birth weight and gestational age were obtained from the primary health center’s information system (SClinico). COVID-19 test results (conducted between March 2020 and June 2022) were obtained from the national surveillance system (SINAVE Lab) and categorized into two primary outcomes: ever positive for COVID-19 (yes/no) and positivity frequency for COVID-19 (count). Robust and standard Poisson regressions were used to estimate the association between primary outcomes and demographic, socioeconomic, and clinical variables. We estimate relative risks (RR) and prevalence ratios (PR) with 95% confidence intervals. Results The positivity rate is lower for immigrant children (12% vs 17%). Compared with non-immigrant, and adjusting for other factors, immigrant children are 52% less likely to be ever positive for COVID-19 (PR = 0.482; IC 95%: 0.392-0.594), and the estimated number of positive tests is 54% lower (RR = 0.456; IC 95%: 0.362-0.574). Conclusions Being an immigrant is a protective factor against testing positive for COVID-19, aligning with the well-known immigrant paradox. These results underscore the need for further research into the immunological profiles of this population and are crucial for guiding strategies to manage emerging public health crises. Key messages • Immigrant children living in the Lisbon metropolitan area may have a protective factor against testing positive for COVID-19, consistent with the well-known immigrant paradox. • Understanding COVID-19 positivity rates and associated factors in children is crucial for guiding effective strategies to manage and mitigate emerging public health crises.