Calcium phosphate (hydroxyapatite or HA) coatings have been applied to Custom Osseous Integrated Implants (COIIs) to improve the quality of the bone-implant integration, yet little is known concerning the biomechanical properties of bone surrounding the HA-coated implants in humans over the long term. The purpose of this study was to characterize the mechanical and histomorphometric properties of the bone along the implant interface. Specimens were prepared from three similar mandibular implants that were functional in three female patients for about 11 years. Histomorphometric analyses showed bone-implant contact averaging 75% for all specimens. Area coverage of residual HA-coating ranged from 52 to 70%. When compared with previous studies, these results show a relatively high percentage of residual HA after a decade in vivo. Nanoindentation showed similar average values of hardness and modulus (p = 0.53 and p = 0.56, respectively) comparing bone adjacent to residual HA-coating and regions where the coating was absent. The elastic modulus was significantly lower for bone near the bone-implant interface (<200 μm) as compared with bone distant (>1000 μm) from the interface (p = 0.05), thereby reflecting different properties of the bone near these interfaces. Backscattered electron imaging showed darker gray levels which indicated decreased mineral content in bone adjacent to the implant, consistent with the nanoindentation results.