Abstract Background Palmitic acid (PA) is predominantly esterified at the SN-2 position of triacylglycerols in human milk. PA at the SN-2 position is more efficiently absorbed and results in reduced formation of PA soaps, as well as reduced fatty acid (FA) and calcium malabsorption. Bovine milk fat (MF), a natural source of SN-2-palmitate, was used in the fat blend of infant formulae (IF) in the current study to investigate its effect on stool fatty acid soaps, calcium excretion and stool characteristics. Methods Two double-blind, randomised cross-over trials (CS1, CS2) were conducted in parallel with healthy term, formula-fed infants aged 9–14 weeks. After a two-week run-in period, infants in CS1 (n = 17) were randomly allocated to receive either a 50% MF-based formula (50MF) or a 100% vegetable fat (VF) formula; in CS2 (n = 18), infants received either a 20% MF-based formula (20MF) or the VF formula, in a 2 × 2-week cross-over design. At the end of each two-week intervention period, stool samples were collected for FA, FA soaps and calcium excretion analysis and stool consistency was assessed according to the Amsterdam Infant Stool Scale (AISS). Results MF-based groups showed no significant difference in PA in stools compared to VF group, although reduced stool PA soaps (CS1: 111.28 ± 18.33 vs. 220.25 ± 29.35 mg/g dry weight, p < 0.0001; CS2: 216.24 ± 25.16 vs. 233.94 ± 35.12 mg/g dry weight, p = 0.0023), total FA soaps and calcium excretion (CS1: 46.40 ± 5.27 vs. 49.88 ± 4.77 mg/g dry weight, p = 0.0041; CS2: 46.20 ± 4.26 vs. 50.47 ± 6.71 mg/g dry weight, p = 0.0067) were observed. Furthermore, the 50MF group showed a favourable lower mean stool consistency score compared to the VF group (1.64 ± 0.49 vs. 2.03 ± 0.19, p = 0.0008). Conclusions While the use of bovine MF in IF did not affect PA concentrations in stool, lower excretion of palmitate soaps, total FA soaps and calcium was seen in healthy term infants. 50MF formula also showed improved stool consistency. The use of MF in IF could be an interesting approach to improve gut comfort and stool characteristics in infants, warranting further research. Trial registration Netherlands Trial Registry Identifier: NTR6702. Date registered: December 01, 2017.