Background: Because of bisphosphonate medication, dental implantation with a subsequent infection poses a relevant risk factor to suffer from medicationrelated osteonecrosis of the jaw. This rat study evaluated different implant materials under systemic bisphosphonate delivery using micro-computed tomography (μCT) images. Methods: Fifty-four rats were randomly allocated into a control group 1, test group 2 with intravenous drug application of zoledronic acid and test group 3 with a subcutaneous application of alendronic acid. After 4 weeks of drug delivery, the first molar on each side of the upper jaw was extracted, and either a zirconia or a titanium implant was immediately inserted. Radiological examinations at four timepoints before the operation, 1 week later, 6 weeks later and after 12 weeks of follow up included μCT measurements of the in vivo peri-implant bone loss. μCT measurements of the ex vivo peri-implant bony structure after 12 weeks follow-up covered the bone mineral density, -volume, -trabecular thickness and -separation. Results: Both test groups showed a significant increase in bone loss over time (P < 0.05). The clinical observations of exposed bone revealed that most cases occurred under alendronic acid delivery. Exposed bone was recorded only in the test groups around both titanium and zirconia implants. Regarding the periimplant bony structure, no significant differences were found between both materials. Conclusions: Systemic bisphosphonate delivery led to increased peri-implant bone loss over time after immediate implant insertion. In terms of bone resorption and bone quality parameters, no implant material was superior to the other.