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BACKGROUND Following HIV-1 infection and antiretroviral therapy, the development of periodontal disease was shown to be favored. However, the influence of HIV-1 infection on the periodontal microbiota after nonsurgical periodontal debridement (NSPD) needs a broad comprehension. This work aimed to compare the subgingival microbiological content of HIV-infected and control patients with periodontitis undergoing NSPD. METHODS The bacterial profile of subgingival biofilm samples of HIV-1-infected (n = 18) and control (n = 14) patients with periodontitis was assessed using 16S rRNA gene sequencing. The samples were collected at baseline, 30 and 90 days after NSPD. The taxonomic analysis of gingival microbiota was performed using a ribosomal RNA database. The microbiota content was evaluated in the light of CD4 cell count and viral load. RESULTS Both HIV and control groups showed similar stages and grades of periodontitis. At baseline, the HIV group showed higher alpha diversity for both healthy (HS) and periodontal sites (PS). Streptococcus, Fusobacterium, Veillonella and Prevotella were the predominant bacterial genera. A low abundance of periodontopathogenic bacteria was observed, and the NSPD induced shifts in the subgingival biofilm of HIV-infected patients, leading to a microbiota similar to that of control patients. CONCLUSION Different subgingival microbiota profiles were identified - a less diverse microbiota was found in HIV-1-infected patients, in contrast to a more diverse microbiota in control patients. NSPD caused changes in the microbiota of both groups, with a greater impact on the HIV group, leading to a decrease in alpha diversity, and produced a positive impact on the serological immune markers in HIV-1-infected patients. Control of periodontitis should be included as part of an oral primary care, providing the oral health benefits and better control of HIV-1 infection. This article is protected by copyright. All rights reserved.