This is a follow-up study to an investigation on the prevalence of malnutrition and micronutrient deficiencies among Vietnamese primary schoolchildren. A total of 454 children aged 7 to 8 years attending three primary schools in the Northern delta province of Vietnam were either provided with regular milk, milk fortified with vitamins, minerals and inulin or served as a reference control group. Children were monitored for anthropometrics, (micro)-nutritional status, faecal microbiota composition, school performance, and health indices. Both weight-for-age (WAZ) and height-for-age (HAZ) significantly improved during 6 months of milk intervention; and underweight and stunting dropped by 10% in these groups. During intervention the incidence of anemia decreased and serum ferritin levels increased significantly in all groups. Serum zinc levels increased and consequently the incidence of zinc deficiency improved significantly in all three groups. Serum retinol levels and urine iodine levels remained stable upon intervention with fortified milk whereas in the control group the incidence of iodine deficiency increased. Bifidobacteria composed less than 1% of the total faecal bacteria. After three months of milk intervention total bacteria, bifidobacteria and Bacteroides sp. increased significantly in both milk and inulin fortified milk groups. Children in the milk consuming groups had significantly better short-term memory scores. Parent reported that health related quality of life status significantly improved upon milk intervention. In conclusion, (fortified) milk consumption benefited the children in rural Vietnam including lowering the occurrence of underweight and stunting, improving micronutrients status and better learning indicators as well as improving the quality of life.