Scope Enhanced adiposity and metabolic inflammation are major features of obesity associated with altered gut microbiota and intestinal barrier. How these metabolic outcomes can be impacted by milk polar lipids (MPL), naturally containing 25% of sphingomyelin, is investigated in mice fed a mixed high‐fat (HF) diet . Methods and results Male C57Bl/6 mice receive a HF‐diet devoid of MPL (21% fat, mainly palm oil, in chow), or supplemented with 1.1% or 1.6% of MPL (HF‐MPL1; HF‐MPL2) via a total‐lipid extract from butterserum concentrate for 8 weeks. HF‐MPL2 mice gain less weight versus HF (p < 0.01). Diets do not impact plasma markers of inflammation but in the liver, HF‐MPL2 tends to decrease hepatic gene expression of macrophage marker F4/80 versus HF‐MPL1 (p = 0.06). Colonic crypt depth is the maximum in HF‐MPL2 (p < 0.05). In cecal microbiota, HF‐MPL1 increases Bifidobacterium animalis versus HF (p < 0.05). HF‐MPL2 decreases Lactobacillus reuteri (p < 0.05), which correlates negatively with the fecal loss of milk sphingomyelin‐specific fatty acids (p < 0.05). Conclusion In mice fed a mixed HF diet, MPL can limit HF‐induced body weight gain and modulate gut physiology and the abundance in microbiota of bacteria of metabolic interest. This supports further exploration of how residual unabsorbed lipids reaching the colon can impact HF‐induced metabolic disorders.