Peri-implantitis is an infectious disease which causes an inflammatory process in soft tissues as well as bone loss around an osseointegrated implant in function. Peri-implantitis should be focused on the control of infection, regeneration of the alveolar bone and detoxification of the implant surface. Incudent tooth paste has antimicrobial, anti-inflammatory and bone regenerative properties. Thus, A study is planned to assess the microbiological outcome of incudent tooth paste in cases with peri-implantitis and with a follow-up period of 7 months. The 30 peri-implantitis patients were selected. After debridement, peri-implantitis cases were treated with incudent tooth paste . The DNA–DNA checkerboard hybridization method was used to detect bacterial presence during the first 360 days of treatment. At 7 day, significantly lower bacterial loads for 30 individual bacteria including Porphyromonas gingivalis, Treponema socranskii, Actinomyces naeslundi type 1, Actinomyces gerensceriae, Actinomyces israelii, Actinomyces naeslundi type 1 and type 2 and Actinomyces odontolyticus were found. At Day 210 the levels of Porphyromonas gingivalis, Treponema socranskii, Actinomyces naeslundi type 1, Actinomyces gerensceriae, Actinomyces israelii, Actinomyces naeslundi type 1 and type 2 and Actinomyces odontolyticus were lower as compared to baseline as well as at 7 day. Incudent tooth paste formulation is very effective against peri-implantitis.