Abstract Background In 2023, 25% of children born in the Lisbon metropolitan area were from foreign mothers. Children of immigrant parents often face an unbalanced diet and unhealthy lifestyle, preventing them from reaching their full potential. The aim of this study was to analyse the associations between migrant status and breastfeeding duration, fruit and vegetable consumption and physical activity in children living in the Lisbon metropolitan area, Portugal. Methods Cross-sequential cohort study in Lisbon Region. Between May 2022 and April 2024, 729 children (49.4% immigrants) born in 2018 and 2020 were enrolled in the study. Data were collected in a face-to-face interview with the parents using a structured questionnaire with information on children’s diet (fruit and vegetable consumption) and physical activity. We used X2, Mann-Whitney U and t-tests to compare immigrant and non-immigrant children. Adjusted odds ratios (aOR) with a 5% level were estimated by logistic regression. Results Immigrant children (49.4%) live in socio-economically disadvantaged families. Breastfeeding practices are more common among migrant mothers with a higher median duration of exclusive breastfeeding (6 versus 4 months, p < 0.001) and a higher median duration of breastfeeding (14 versus 8 months, p < 0.001). Parental migration background is associated with the frequency of fruit (p = 0.039) and vegetable (p < 0.01) consumption and with the practice of physical activity (p < 0.01). The odds of consuming three or more portions of fruit are 1.37 times higher for non-immigrant children, and the odds of consuming two portions of vegetables are higher for non-immigrants than immigrants (aOR=2.04, p < 0.01). Practicing sports is most frequent in non-immigrants (aOR =2.25; p < 0.01). Conclusions Migrant status was associated with a less healthy lifestyle in childhood for children living in the Lisbon metropolitan area. Key messages • Breastfeeding is an essential source of nutrition for children, especially in socio-economically disadvantaged families. • The migrant status is often associated with inequalities in childhood, challenging immigrant children to achieve their full potential.