Background: The modern broiler or meat chicken has ongoing bone health problems. Phosphorus (P) plays an important role in bone development and increased understanding of P metabolism should improve the skeletal health of broilers. Enterococcus faecium has been widely used as a probiotic in broiler production and shown to improve skeletal health of rats; but its effect on the bones of broilers remains unclear. This study investigated the effect of E. faecium on P absorption and utilization in broilers and associated changes in the gut microflora using 16S rDNA sequencing.Results: Dietary supplementation with E. faecium improved P absorption through up-regulation of the expression of intestinal NaP-IIb mRNA, and increased the concentration of serum alkaline phosphatase. These actions increased P retention and bone mineralization in E. faecium treated broilers. The positive effects of E. faecium on P metabolism were associated with changes in the structure of the intestinal microbiota. There was increased relative abundance of the following genera, Alistipes, Eubacterium, Rikenella and Ruminococcaceae, and a decrease in the relative abundance of Faecalibacterium and Escherichia-Shigella. Conclusions: Dietary supplementation with E. faecium changed gut microbiota structure of broilers, increased the relative abundance of SCFA (short chain fatty acid) producing bacteria, improved intestinal P absorption, bone forming metabolic activities, and decreased P excretion. E. faecium facilitates increased utilisation of P in broilers.