Post-implantation failure associated with insufficient host tissue integration at the bone-implant interface and aseptic loosening is a major concern in orthopaedics as well as in dentistry. To overcome the failure in early stages of implantation, prosthetic design combining the mechanisms of porosity guided bone ingrowth along with topographic manipulation of osteogenic cells over bacterial colonization would be an ideal choice, although achieving such a goal is highly challenging. In this study, facile rapid hydrothermal synthesis of nanostructures with simultaneous deposition of hydroxyapatite on the titanium alloy surface was demonstrated by using an aqueous sodium tripolyphosphate and calcium hydroxide mixture. Nanostructures with wire-like morphology exhibited significantly higher osteogenic related gene expression (COL I, OPN, and OCN) through differentiation of adipose derived mesenchymal stem cells as well as the bactericidal response against S. aureus and E. coli as compared to other nanotopographic features. The same also exhibited elongated cell morphology with the highest expression of paxillin towards cell boundaries as compared to the polished surface with flattened cell morphology and localized expression of paxillin around the nucleus. Implantation of treated porous Ti6Al4V samples representing a multiscalar hierarchy with wire-like nanostructures accelerated osteochondral healing in rabbits without any major signs of infection. Also, significantly higher bone formation was observed within the defects implanted with treated porous Ti6Al4V (44.0%) as compared to that of untreated porous samples (36.9%) as well as empty defects (19.6%).