Children of migrant families are known to be at a higher risk of diet-related morbidities due to complex variables including food insecurity, cultural and religious beliefs, and sociodemographic factors like ethnicity, socioeconomic status, and education. Several studies have assessed the presence of specific diseases related to dietary issues in migrant children. This systematic review aims to highlight the existing body of work on nutritional deficiencies in the specific vulnerable pediatric population of immigrants. Refugees were intentionally excluded because of fundamental differences between the two groups including the reasons for migration and health status at the time of arrival. A total of 29 papers were included and assessed for quality. Most of them described a strong correlation between obesity and migration. A high prevalence of stunting, early childhood caries, iron and vitamin D deficiency was also reported, but the studies were few and heterogeneous. Food insecurity and acculturation were found important social factors (nevertheless with inconclusive results) influencing dietary habits and contributing to the development of morbidities such as obesity and other metabolic disorders, which can cause progressive unsustainability of health systems. Public health screening for diet-related diseases in migrant children may be implemented. Educational programs to improve children’s diet and promote healthy-living behaviors as a form of socioeconomic investment for the health of the new generations may also be considered.