Literature is scarce on food insecurity in the context of different illnesses and intersecting social hierarchies of gender and ethnicity. This study aims to describe and compare the prevalence of food insecurity between immigrants and natives in Portugal and explore social determinants of poor health outcomes associated with food insecurity. Data were derived from the National Food, Nutrition and Physical Activity Survey 2015–2016, which is a national and regionally representative survey of the Portuguese general population which collected nationwide data on dietary habits (including food insecurity measured by the Radimer/Cornell food security questionnaire) and physical activity, among other dimensions. Demographic, socioeconomic and health factors that could help explain ethnic disparities in food insecurity were explored through complex survey data analysis. The prevalence of food insecurity was 10.7% (95% CI: 6.5–15.0) among immigrants and 10.1% (95% CI: 8.3–11.9) among natives; no significant differences were found. Low family income and low level of education were the main factors associated with food insecurity in Portugal, in both native and immigrant groups. Self-reported diseases and poor self-rated health were also associated with food insecurity. Only among natives, women, older and unmarried subjects had higher food insecurity. Therefore, inter-sectoral policies addressing the social determinants of food insecurity are needed to reduce social inequalities and particular attention should be given for Portuguese women, elderly and unmarried people which are the most vulnerable groups. Promoting equality in household food and nutrition security in Portugal including among immigrant’s populations is a public health priority.