In sub-Saharan Africa, one of the most popular contraceptives of choice is depo-medroxyprogesterone acetate (DMPA). In many observational studies, DMPA has been associated with an increased acquisition risk of HIV in comparison to other hormonal contraceptives (HC). The recent ECHO (Evidence for Contraceptive options and HIV Outcomes) trial was a clinical trial designed to directly answer the question by randomizing women to three contraceptive types: DMPA-IM (Intramuscular), Copper IUD, and the LNG (Levonorgestrel) Implant. However, this trial found no difference in HIV incidence rates between contraceptive types. Nevertheless, there is an intense debate over concerns regarding the effect of HC’s and DMPA on the mucosal biology of the female genital tract. This thesis is an examination of vaginal mucosal biospecimens from a subset of women who were enrolled in the ECHO trial. Here, we performed mass spectrometry-based proteomic analysis of cervicovaginal soft-cup samples from a subset of women from clinical sites in South Africa and Kenya, for baseline and 1-month post contraception initiation time points, to examine changes to the mucosal proteome and microbiome. Proteome changes associated with DMPA-IM revealed a decrease in proteins involved with innate immune response, with no changes to the vaginal microbiome. Minor changes to the proteome with LNG implant use were observed which precluded pathway analysis. Additionally, no significant changes to the vaginal microbiome were observed. The largest proteome changes were observed with Copper IUD use and included increased immune cell chemotaxis and complement activation, with a decrease in factors relating to cell-cell adhesion and keratinocyte differentiation. The bacterial component of the vaginal microbiome was significantly impacted with Copper IUD use, showing a significant increase in alpha-diversity with a decrease in Lactobacillus and L. iners and an increase in Prevotella and Sneathia species. Additionally, we performed a case-control sub-analysis of women who seroconverted in each contraceptive arm. Proteomic analysis revealed no significant difference to the vaginal microbiome. However, host proteomic signatures associated with cell-cell adhesion were observed to increase amongst HIV seroconverters, which was observed to overlap with signatures identified with Copper IUD use. This research contributes to the discussion on vaginal health and the impact of contraceptives with insight into potential mechanisms associated with HIV incidence.