The vaginal composition of African women is more often lactobacillus-deficient compared to that of women from other areas around the world. Lactobacillus-deficient microflora is a known risk factor for serious health problems, such as preterm birth, cervix cancer, and entrapment of human immunodeficiency virus (HIV) and other sexually transmitted infections (STIs). The aim of this study was to assess the effect of local vaginal antibiotic or antiseptic treatment on abnormal vaginal flora (AVF), aerobic vaginitis (AV), and bacterial vaginosis (BV) among women in rural, semi-urban, and urban areas in Uganda, as compared to placebo. In a double-blind, placebo-controlled, randomized trial, 300 women presenting for outpatient routine, follow-up, or medical care at Mulago Hospital in Kampala, Uganda, were enrolled to receive 6 days of treatment with vaginal rifaximin (RFX), dequalinium chloride (DQC), or placebo if they had an increased vaginal pH of >4.5 as determined by self-testing. At initial visit and at control visit after 4 weeks, a smear was taken for blinded wet mount microscopy to determine AVF, BV, AV, and Candida severity scores. As compared to placebo, both RFX or DQC treatments dramatically diminished BV prevalence and severity from the initial to follow-up visit: the BV score declined from 2.5 to 1.6 (p < 0.0001) and from 2.5 to 1.9 (p < 0.0001), respectively. Similarly, strong improvements in the AV score were seen in both treatment regimens: moderate and severe AV declined from AV scores of 6.3 to 3.6 (p = 0.003) and from 6.6 to 4.1 (p < 0.004), respectively. Also, women with AVF (deceased or absent lactobacilli) showed similar improvements when compared with placebo. Women with normal flora and Candida at the initial visit showed less Candida after 4 weeks in the group treated with DQC (p = 0.014). Even after a short duration of intravaginal treatment with local non-absorbable antiseptics or antibiotics produced significant, lasting improvements in the vaginal microbiome composition of women with disturbed vaginal microflora. As African women have high prevalences of BV, AV, and AVF, this approach could improve their odds to prevent health-compromising complications. Further studies assessing direct health outcomes are needed to substantiate this.