Our team has been working for some time on designing a new kind of biomimetic fixation of resurfacing endoprostheses, in which the innovative multi-spiked connecting scaffold (MSC-Scaffold) that mimics the natural interface between articular cartilage and periarticular trabecular bone in human joints is the crucial element. This work aimed to develop a numerical model enabling the design of the considered joint replacement implant that would reflect the mechanics of interacting biomaterials. Thus, quantitative micro-CT analysis of density distribution in bone material during the embedding of MSC-Scaffold in periarticular bone was applied. The performed numerical studies and corresponding mechanical tests revealed, under the embedded MSC-Scaffold, the bone material densification affecting its mechanical properties. On the basis of these findings, the built numerical model was modified by applying a simulated insert of densified bone material. This modification led to a strong correlation between the re-simulation and experimental results (FVU = 0.02). The biomimetism of the MSC-Scaffold prototype that provided physiological load transfer from implant to bone was confirmed based on the Huber–von Mises–Hencky (HMH) stress maps obtained with the validated finite element (FE) model of the problem. The micro-CT bone density assessment performed during the embedding of the MSC-Scaffold prototype in periarticular bone provides insight into the mechanical behaviour of the investigated implant-bone system and validates the numerical model that can be used for the design of material and geometric features of a new kind of resurfacing endoprostheses fixation.