Clinical and laboratory studies were conducted in 24 patients with chronic dental periimplantitis before and after complex treatment aimed at destroying biofilms on the surface of the dental implant to prevent indirect infection. The aim of the study is to develop a comprehensive, etiologically based treatment regimen for dental peri-implantitis based on correction of the oral microbiota. The study was based on indicators of secretory immunoglobulin A (IgA) and an analysis of the composition of the microbiome of mixed saliva in patients with healthy implants and peri-implantitis. A new conceptual approach to the diagnosis and pathogenetically based comprehensive treatment of dental peri-implantitis is proposed. At the first stage, a peri-implantitis treatment regimen was performed according to the protocol “The EFP S3 level clinical practice guideline”. After performing this standard treatment for 6 weeks, we have proposed a scheme that includes: 1) the drug for inhibiting the bacterial film “ACC LONG” 600 mg (Hermes Pharma, Germany) – in the form of oral baths for 2 minutes 30 minutes before meals; 2) for the purpose of adhesion and sorption of biofilm elements – Chitosan succinate (Active+ drug, GREEN VOICE, Russia) after meals in rinsing method: dosage of 10–12 drops per 250 ml of liquid; 3) for the purpose of probiotic correction of oral microbiocenosis, the drug BIFIDUM BAG (5 ml dissolved in water no higher than 40 °C) for 20–30 minutes topically in the form of mouth baths, then swallow after eating for one month. It was found that with the progression of peri-implantitis, there is a decrease in the level of secretory IgA and a decrease in local resistance of the oral cavity to pathogenic influences. The standard treatment regimen helps to stabilize inflammation in the area of dental implants, but does not lead to a sustained positive effect.