BACKGROUND: Changes in the oral microbiome are expected in the presence of chronic conditions such as type 2 diabetes mellitus (T2D), arterial hypertension (AH), and obesity (OB). OBJECTIVE: We aimed to map the literature regarding oral microbiome changes in people with T2D, AH, or OB compared to those without these conditions. METHODS: This scoping review was guided by the JBI Manual for Evidence Synthesis and reported according to the PRISMA extension for scoping reviews (PRISMA-ScR). A search strategy was developed and adapted to five databases (Embase, LILACS, PubMed, Scopus, and Web of Science) and gray literature (Google Scholar and ProQuest Dissertation and Thesis). Two reviewers individually screened studies for inclusion. Data from the studies, including the molecular method to evaluate the microbiome and the type of sample, were extracted and analyzed. The focus was significant changes in phylum and genera. RESULTS: A total of 1413 records were retrieved from databases, 86 from gray literature, and 7 from reference lists. After the screening process, 50 records were included, 28 on T2D, 8 on AH, and 12 on OB. Two studies addressed metabolic syndromes. Most studies identified the oral microbiome in saliva using 16S rRNA amplicon sequencing. CONCLUSION: At the phylum level, Fusobacteria was enriched in ≥3 studies in people with T2D. Firmicutes enrichment was associated with T2D and OB. Genera enriched in T2D comprised Catonella, Leptotrichia, Prevotella, and Rothia. Aggregatibacter and Prevotella were enriched in OB. No phylum or genera were consistently enriched in AH.OSF protocol registration: DOI 10.17605/OSF.IO/XK72V (available at https://osf.io/z5fp4 ).