Portugal has one of the highest rates of childhood overweight and obesity in Europe. However, little is known about the health of ethnic minorities living in its capital city, Lisbon. The Cape Verdean community in Lisbon tend to have low educational levels, material deprivation and struggle with discrimination and racism, factors that would probably be associated with a higher prevalence of overweight and obesity. Data for the Cape Verdean population were collected in three different time periods by three different research teams in 1993, 2009 and 2013 and included children aged 6–12 years living in the Cova da Moura neighbourhood of the Greater Lisbon Metro Area. The Portuguese national survey was conducted between 2009 and 2010 at public and private schools in mainland Portugal and included height, weight, skinfolds and arm and waist circumferences. From these survey data body mass index (BMI) and prevalence of stunting (chronic malnutrition – low height-for-age) and underweight (low weight-for-age) were calculated according to reference values proposed by Frisancho (2008). Overweight and obesity prevalence values were defined based on the references established by the International Obesity Task Force. The results show significant differences in height between Cape Verdean and Portuguese boys and girls. Generally, Cape Verdeans’ growth falls within the healthy range of international growth references across all of the survey data collected. Cape Verdean rates for combined overnutrition (overweight and obesity) in 2013 (9.8% for boys and 16.7% for girls) were lower than those of the Portuguese (33% for boys and 31.7% for girls). Logistic regression models showed that Cape Verdean children had a lower risk of being overweight or obese when accounting for breast-feeding, birth weight, maternal education and occupation. Despite living in a deprived neighbourhood these Cape Verdean children seemed to have grown more healthily than Portuguese ancestry children. The challenge for policymakers will be to support improvement of the poverty-related living conditions of this community without creating a risky environment for increasing prevalence of overweight and obesity.