This study aimed to examine differences in all-cause mortality and main causes of death across different migrant and local-born populations living in six European countries. We used data from population and mortality registers from Denmark, England & Wales, France, Netherlands, Scotland, and Spain. We calculated age-standardized mortality rates for men and women aged 0–69 years. Country-specific data were pooled to assess weighted mortality rate ratios (MRRs) using Poisson regression. Analyses were stratified by age group, country of destination, and main cause of death. In six countries combined, all-cause mortality was lower for men and women from East Asia (MRRs 0.66; 95 % confidence interval 0.62–0.71 and 0.76; 0.69–0.82, respectively), and Other Latin America (0.44; 0.42–0.46 and 0.56; 0.54–0.59, respectively) than local-born populations. Mortality rates were similar for those from Turkey. All-cause mortality was higher in men and women from North Africa (1.09; 1.08–1.11 and 1.19; 1.17–1.22, respectively) and Eastern Europe (1.30; 1.27–1.33 and 1.05; 1.01–1.08, respectively), and women from Sub-Saharan Africa (1.34; 1.30–1.38). The pattern differed by age group and country of destination. Most migrants had higher mortality due to infectious diseases and homicide while cancer mortality and suicide were lower. CVD mortality differed by migrant population. To conclude, mortality patterns varied across migrant populations in European countries. Future research should focus both on migrant populations with favourable and less favourable mortality pattern, in order to understand this heterogeneity and to drive policy at the European level.