This study evaluated the effects of antimicrobial photodynamic therapy (aPDT) in the alveolar repair of rats with major risk factors for bisphosphonate-related osteonecrosis of the jaws (BRONJ). Senile rats received 0.45 ml of vehicle (VEH and VEH/aPDT) or 0.45 ml of zoledronate (ZOL and ZOL/aPDT) every three days for seven weeks. After three weeks of treatment, the first lower left molar was extracted. VEH/aPDT and ZOL/aPDT were submitted to aPDT on the extraction site at 0, 2 and 4 days postoperatively. Euthanasia was performed 28 days postoperatively and the extraction site was evaluated by clinical, histological, histometric, histochemical and immunohistochemical analysis. ZOL showed tissue repair impairment; lower percentage of newly formed bone tissue (NFBT); higher percentage of non-vital bone tissue (NVBT); fewer mature collagen fibers and increased immunolabeling for tumor necrosis factor (TNFα), interleukin (IL)-1β and IL-6. ZOL/aPDT showed clinical and histological characteristics of the extraction site, percentage of NFBT and percentage of mature collagen fiber similar to VEH. Percentage of NVBT and immunolabeling for inflammatory cytokines in ZOL/aPDT was lower than in ZOL. Immunolabeling for tartarato-resistant acid phosphatase (TRAP) was lower in ZOL and ZOL/aPDT. aPDT in the dental extraction site improves tissue repair process and prevents the occurrence of BRONJ-like lesions after tooth extraction. •Bisphosphonate-related osteonecrosis of the jaws (BRONJ) is a serious adverse effect of therapies with anti-resorptive drugs.•BRONJ is a difficult to treat condition.•Antimicrobial photodynamic therapy (aPDT) was effective, safe and able to prevent the occurrence of BRONJ-like lesions in rats.