Bone defects account for a significant proportion of surgeries, increasing healthcare costs and complicating therapies. These factors necessitated cell-instructive bioengineering procedures to support and restore pre-existing bone function. Herein, iron-reinforced hydroxyapatite nanorod was used as an inorganic component, collagen/polycaprolactone was used as an organic component, and tannic acid was used as a surface modifier (onto nanorods), crosslinker, and functional agent. The inorganic–organic nanofibers were coated onto an implant surface using electrospinning. The nanocomposite nanostructural, contact angle, surface chemistries, thermomechanical, physicochemical, cytocompatibility, antioxidant potential, aspects of osseointegration ranging from cell adhesion, proliferation, differentiation, and bone remodeling at bone-implant zone in a rat model were studied. The results support that metal-phenolic networks on nanorods regulate interfacial interactions, nanorods cytocompatibility, antioxidant potential, and phase compatibility between organic and inorganic materials of scaffolds. The organic/inorganic nanocomposite better mimicked the bone matrix and better-supported MC3T3-E1 cell attachment, proliferation, matrix mineralization (intracellular alkaline phosphatase and calcium accumulation), and osteogenic gene expression (OPN, OCN, COL1A2, and RUNX2) to direct cell fate for bone reconstruction than its counterpart organic scaffold. The active bone formation and rebuilding of the bone-implant zone in rat models confirmed the bioactive potential of the studied nanocomposite, and it thus could be used as an interface scaffold to boost osteointegration.