Background This study aimed to evaluate the vaginal microbiota of HIV‐positive pregnant women relative to HIV‐negative controls, and to compare their risk of vaginal dysbiosis, bacterial vaginosis, and vulvovaginal candidosis (VVC). Methods This is a nested matched case‐control study that analyzed data from women who received pregnancy care at our center from 2003 to 2014. Women routinely underwent screening for asymptomatic vaginal infections using phase microscopy on Gram‐stained smears. HIV‐positive women were assigned to the case group, and HIV‐negative women were assigned to the control group. Cases and controls were matched in a 1:4 ratio. Logistic regression was used to test whether HIV infection was associated with vaginal dysbiosis (Nugent score 4‐6), BV (Nugent score 7‐10), or VVC. Results One hundred and twenty‐seven women were assigned to the case group, and 4290 were assigned to the control group (including 508 matched controls). Dysbiosis or BV was found in 29.9% of the cases and 17.6% of the controls. Women in the case group had increased risk of vaginal dysbiosis or BV (odds ratio [OR] 2.09, 95% confidence interval [CI], 1.30‐3.32, P = .002). The risk of VVC was also higher in the case group (OR 2.14, 95% CI, 1.22‐3.77, P = .008). The incidence of preterm birth did not differ significantly between the groups (cases: 8.7%; controls: 10%, P = .887). Conclusions HIV‐positive women are at risk of vaginal dysbiosis, BV, and VVC during pregnancy. As imbalances of the vaginal microbiota can lead to preterm birth, screening and treatment of HIV‐positive pregnant women are warranted.