In this work we studied the main surface characteristics together with the in vivo osseointegration of three Zr-Ti alloys with hydroxyapatite-zirconia-silver (HAP-ZrO2-Ag) coating layer. The main purpose was to provide a quantitative evaluation and interpretation from micro to nano scale of the processes involved in the osseointegration of the HAP-ZrO2-Ag coated Zr-Ti specimens in a pig model. The surface characteristics were studied by scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), and X-ray diffraction (XRD). After the insertion of the implants into pig tibia, the osseointegration was investigated by means of biochemical analysis as well as bone histomorphometric and computed tomography measurements. The results of this in vivo study sustains that the capacity of the Zr-Ti specimens coated with HAP-ZrO2-Ag to promote osteogenesis is significant during the first month after implantation as compared with the control, being influenced by the interactions between bone tissue and HAP-ZrO2-Ag surfaces, but also by the chemical composition of the alloys.