The impact of non-communicable diseases (NCDs) is disproportionately felt by immigrants from low- to medium-income countries (LMICs), partly due to their dietary habits. To thrive in their new environment, migrants either omit or consume certain food items, which could lead to nutritional deficits. As a result, most migrants experience more NCDs than their compatriots in their native countries. Therefore, we evaluated the difference in dietary habits, quality, and the influencing factors of overweight or obesity among African migrant students in Nanjing (China) and non-migrant students in Africa using cross-sectional data. The researchers used the food frequency questionnaire and the global diet quality score metrics to assess food intake and quality, respectively. Then, cross-tabulation was employed to explore the differences between the groups in meal skipping, eating habits, and diet quality. Finally, the factors associated with overweight or obesity were assessed with binary logistic regression stratified by African students in Nanjing and students in their native countries. Approximately 678 responses were received, mainly between 18-25 years (46.7%) and 26-36 years (45.4 %). The majority of them (52.3%) were international students. The non-migrant African students' diets lacked citrus fruits (22.2%), deep orange fruits (15.4%), deep orange vegetables (18%), cruciferous vegetables (24.6%), and dark leafy vegetables (26.5%). While the African migrant students consumed more high-fat dairy (50.7%), processed meats (23.9%), sweets and ice creams (51.3%), sugar-sweetened beverages (40.5%), and juice (61.5%), p < 0.001. Furthermore, consuming late-night meals constantly [Exp (B) = 39.607, p = 0.049], eating twice a day [Exp (B) = 6.527, p = 0.036], consuming red meat [Exp (B) = 29.287, p = 0.001], processed meats [Exp (B) = 719.979, p = 0.0011], refined grains and baked foods [Exp (B) = 15.752, p = 0.013], and sweets and ice cream [Exp (B) = 193.633, p = 0.006] were factors inducing overweight or obesity among only African migrant students. Controlling the what (Western diet and nature of late-night meals) and the when of eating can drastically reduce their influence on obesogenic condition formation in African migrant students in China and elsewhere.