Background and Objectives: Maternal nutrition affects fetal growth and development. This study evaluates the effects of milk powder fortified with micronutrients, docosahexaenoic acid (DHA), a prebiotic, and probiotic Bifidobacterium animalis subsp. lactis HN019 DR10(TM) on the micronutrient status, as well as the presence of faecal probiotic and immune markers in pregnant women. Methods and Study Design: This randomised, double-blind, placebo-controlled trial was conducted at Budi Kemuliaan and Cipto Mangunkusumo Hospital in Jakarta from 2013 to 2014. A total of 104 participants were randomly allocated to receive either completely enriched milk powder (intervention group) or iron- and vitamin folic-acid-enriched milk powder (control group). Data were collected using standardised measures and were statistically analysed using the independent t or Mann Whitney test. Results: At the baseline, the micronutrient status of the participants was acceptable, except for 25-OH-vitamin D, in both the intervention and control groups. Vitamin B-1, zinc, total free fatty acid, linoleic acid, arachidonic acid, and DHA were significantly higher in the intervention group in the second trimester (p=0.014, 0.028, 0.023, 0.014, 0.001, and 0.032, respectively). Interleulcin-6 and tumor necrosis factor-alpha levels did not significantly vary during pregnancy. B. animalis subsp. lactis DR10(TM) was present in the faeces of the intervention group but not the control group (61.1% vs 0%). Conclusion: Milk fortified with a prebiotic, probiotic, DHA and micronutrients increases the faecal concentration of the organism used for fortification in Indonesian pregnant women. This may represent an improvement in intra-partum maternal gut health.