The objective of this study was to investigate the dietary effects of fermented Broussonetia papyrifera (FBP) on serum biochemistry, mineral deposition, and intestinal microbiota in finishing pigs. Thirty-six grower pigs (18 males and 18 females, with an initial body weight of 12.25 ± 0.15 kg) were selected and randomly assigned to two dietary treatment groups: CON group fed a basal diet, and treatment group fed an isonitrogenous and isocaloric FBP diet (20% FBP). Each treatment included 6 replicates with 3 pigs in each replicate, and the feeding trial lasted 6 months. The results showed that dietary FBP significantly reduced ammonia, alanine aminotransferase, aspartate aminotransferase and urea nitrogen in the serum of finishing pigs. In addition, the FBP diet significantly reduced the concentration of iron, calcium, magnesium, zinc, and manganese in serum, as well as magnesium and manganese levels in faeces, while significantly increasing selenium, copper, and iron concentrations in the liver and iron and selenium in muscles. Dietary FBP raised the abundance of Terrisporobacter, Clostridium butyricum, Akkermansia, and Turicibacter, while decreasing the abundance of Lactobacillus in the colon. The abundance of Unclassified_k_ norank_d_Bacteria was closely related to iron and magnesium concentrations. In conclusion, these results suggest that the dietary effect of FBP on absorption, metabolism and deposition of minerals could be attributed to an altered microbial community in the colon. We recommend further studies to unravel the underlying mechanisms by which gut microbes modulate mineral deposition.