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Background: Vaginal microbiota dysbiosis could lead to the vaginal health conditions. This imbalance in vaginal microbiota can be due to a number of factors including contraceptive methods. Objective: This study was carrried out to investigate the vaginal microbiota dysbiosis and associated vaginal health outcomes among women under contraception at Musasa health Center. Materials and Methods: This was a cross sectional study. 56 vaginal swab samples were collected from women enrolled in a family planning program, and transported to INES Ruhengeri clinical microbiology laboratory for vaginal microbial community analysis. The outcomes were evaluated by scheduled interviews. Chi square test was used to evaluate association of microbiota imbalances in the vagina and the vaginal health outcomes. Results: Lactobacilli (92.85%) was the most predominant microorganism observed in the vagina. Outcomes of the vaginal microbiota dysbiosis under different contraceptive regimes were observed. Vaginal microbial community imbalance in different family planning methods was statistically significant (x2 = 36.5, P = 0.049048) to be associated with vaginal health outcomes such as bacterial vaginosis, urinary tract infections, candidiasis and vaginitis. The association with contraceptives contraceptive methods and vaginal microbial community dysbiosis was statistically significant (x2 = 96.2403, P = 0.000491). The Implant for 5 years and Intrauterine device (IUD) were statistically significant (x2 = 28.533, P = 0.002681 and x2 = 27, P = 0.004595 respectively) to contribute to the vaginal microbiota balance. Conclusion: This study established that family planning methods could cause vaginal dysbiosis thereby exposing the vagina to adverse health outcomes and poor reproductive health. Women undergoing family planning should seek medical support if any sign of vaginal infection is observed.