Background: Natural enrichment of sn-2 palmitate content of infant formulae by using bovine milk fat is known to reduce faecal fatty acid soap formation and improve stool consistency, but effects on gut microbiota composition are unknown. The purpose of this study was to test the influence of milk fat-based formula high in sn-2 palmitate on the infants’ gut microbiota composition and to confirm the beneficial effects of the formula on faecal composition and stool consistency. Methods: Twenty-two healthy term, formula-fed infants were enrolled in a single-blinded randomized, crossover, placebo-controlled trial. After a 2 week run in period, infants received either a 50% milk fat-based formula containing 39% sn-2 palmitate (MF) or a vegetable fat-based formula (VF) containing 10% sn-2 palmitate in a 2x2 week crossover design. Faecal microbiota composition was the primary outcome of the study. Other outcomes included faecal fatty acid soap excretion, calcium excretion, gut comfort parameters and faecal metabolites. Results: Microbiota analysis showed that bifidobacteria dominated the gut microbiota of most infants. Neither alpha- nor beta-diversity was significantly influenced by the intervention. The MF formula resulted in significantly lower faecal levels of palmitic acid soap and total fatty acid soaps than the VF formula (p<0.0002). Additionally, calcium excretion and palmitic acid concentration were significantly (p<0.05) lower in stool samples after MF intervention. Furthermore, a significant physiological effect on softer stools was observed in the MF intervention compared to the VF intervention (p=0.02). Of the 870 measured faecal metabolites, 263 were significantly different after MF and VF intervention (p<0.05). Most of these were found at higher levels after MF intervention, potentially indicative of the complex structure of milk fat. Metabolites with more than 2-fold change between interventions were mostly lipid-derived and included several milk fat-specific fatty acids. Conclusions: Replacing part of the vegetable fat in infant formula with bovine milk fat with high sn-2 palmitate levels did not change the microbiota composition, although a reduction in faecal palmitate soaps, total fatty acid soaps and calcium excretion while improving stool consistency in the MF intervention was confirmed. In addition, 263 faecal metabolites were significantly different, many related to the fat source. Trial registration: Netherlands Trial Registry Identifier: NL7815 19/06/2019