The objective of this study was to assess the effect of a novel corn-expressed phytase (CEP) on growth, nutrients digestibility, bone characteristics and fecal microbiota of pigs fed with very low-protein, -calcium (Ca) and -phosphorous (P) diets. Forty-eight barrows were subjected to 6 groups for 4 weeks: positive control-adequate protein (PC), negative control-reduced protein (NC), NC + low-dose CEP, i.e., 2000 FTU/kg (LD), NC + high-dose CEP, i.e., 4000 FTU/kg (HD), LD with 0.12% unit reduced Ca and 0.15% unit reduced available P (LDR), and HD with 0.12% unit reduced Ca and 0.15% unit reduced available P (HDR). Compared to NC, LD and HDR had a higher average daily gain (ADG) and gain:protein ratio (G:P), HD and HDR had greater apparent fecal digestibility of Ca and P and bone mineral density and LDR and HDR had lower serum osteocalcin. The feces of LD was enriched in Lachnospiraceae, while the HD had a higher abundance of Succinvibrio and LDR had a higher abundance of Bifidobacterium and Actinobacteria. In conclusion, supplementation of protein-restricted diets with a CEP decreased their negative effects on ADG and G:P ratio, increased the digestibility of Ca and P regardless of the levels of these minerals in the diet, improved bone characteristics and produced differential effects on fecal bacterial population.