Adequate calcium intake and supply of vitamin D during childhood play important roles in ensuring adequate bone mass gain to achieve optimal peak bone mass. The Healthy Immigrant Children study employed a mixed-method cross-sectional study design to characterize the health and nutritional status of 300 immigrant and refugee children aged 3–13 years who had been in Canada for less than 5 years. This paper presents bone mineral content and vitamin D status data along with qualitative data that deepen the understanding of newcomer bone health status. A significantly higher percentage of refugee children (72.3%) had insufficient (<50 nmol/L) or deficient (<30 nmol/L) serum vitamin D compared with immigrants (53.2%). Vitamin D deficiency was most common among ethnic minority girls. Newcomer children with higher intakes of vitamin D, younger newcomer children, and those from western Europe or the United States had higher serum vitamin D levels. Immigrants had significantly higher mean total body bone mineral content compared with refugees. Total body fat, serum vitamin D, calcium intake, height, height by calcium intake, total body fat by calcium intake, and total body fat by height predicted total body bone mineral content levels. Vitamin D deficiency among newcomer children may be related to lack of knowledge regarding children’s vitamin D requirements in the Canadian environment, dietary habits established in country of origin, low income that limits healthy dietary choices, and lifestyle habits that limit exposure to sunlight. Results suggest a need to screen newcomer children and pregnant women for vitamin D deficiency and support early intervention.