We hypothesized that the different post-implantation healing stages between the conventional and immediate implantations produce different amounts and tissue composition of the peri-implant bone. Thus, the objective of the current study was to examine whether the stability of dental implant systems is associated with characteristics of the interfacial bone area at different post-implanation healing periods. Mandibular molars were extracted from each beagle dog. After 10 weeks post-extraction, a screw-type titanium dental implant was placed in the molar location following a conventional dental implant (Con) procedure. Simultaneously, mandibular premolars were extracted and the same type of dental implant was placed in the distal site of the extracted premolar root following an immediate dental implant (Imm) procedure. The implant stability quotient (ISQ) values were not significantly different between Con and Imm groups at 0-, 3-, and 6-weeks post-implantation. However, 3D micro-computed tomography and 2D histological images confirmed that the Imm system had more gaps between the bone and implant than the Con system. On the other hand, the nanoindentation modulus value at the bone–implant interface was significantly higher for the Imm group than the Con group at both 3 weeks and 6 weeks post-implantation. The current results from multi-scale characterization suggest that the higher interfacial bone quality of the Imm system, despite its earlier post-implantation stage, plays a crucial role in maintaining stability comparable to that of the Con system.