Cardiovascular disease (CVD), the leading cause of global mortality, is intrinsically linked to atherosclerosis. Recent research suggests that respiratory function may be associated with the development of atherosclerosis. Alterations in the composition of the respiratory microbiome can negatively affect pulmonary function, which in turn may impact cardiovascular health through mechanisms that remain incompletely understood. To analyze the upper airway microbiome abundance and diversity in adults with subclinical atherosclerosis. A case–control study was conducted for atherosclerosis. Oropharyngeal swab samples were collected from participants in the CaRes cohort, for whom carotid Doppler, spirometry, blood chemistry, and clinical history data were available. Sequencing of the 16S ribosomal RNA gene was performed, followed by comparative analyses between subjects with and without atherosclerosis. A total of 100 subjects were analyzed (50 cases and 50 controls). The phylum Bacteroidetes was the most prevalent in both groups, followed by Firmicutes and Proteobacteria. Family Enterobacteriaceae was more abundant among case group, which included species such as Serratia, Klebsiella spp., and Campylobacter. Evaluation of alpha diversity indices revealed lower levels for cases group, with a Shannon diversity index of 2.61 compared to 4.07 in controls (p = 0.006). Differences in microbiota composition were observed between cases and controls. Specifically, the family Enterobacteriaceae was associated with the presence of atherosclerosis, suggesting its potential involvement in the progression of cardiovascular disease.