Background: Injectable depot medroxyprogesterone acetate (DMPA) is the most common contraceptive choice among young women in Uganda, where HIV burden is high and HIV pre-exposure prophylaxis (PrEP) may be offered. For young women who choose to use both agents concurrently, it is unknown whether they will experience declines in BMD beyond those elicited by either product singly. Methods: From 2018–2022, we conducted a 2-year prospective study with women ages 16–25 years in Kampala, Uganda desiring pregnancy and HIV prevention. Women were provided condoms, injectable DMPA, and/or FTC/TDF, according to their choices and underwent annual dual x-ray absorptiometry (DXA) scans. We used tenofovir-diphosphate (TFV-DP) quantification in dried blood spots and DMPA injection dates to classify exposure. Linear regression models estimated the difference in % BMD change from baseline to month 12 for women using FTC/TDF and DMPA versus women using neither product. Results: Of 499 enrolled women, discontinuation and re-starting of contraception and PrEP was common. Women consistently using neither product (n = 39) experienced BMD increases. Women with consistent use of both products during 1 year (n = 22) experienced an average BMD loss of 1.04% at lumbar spine and hip and 1.77% at femoral neck. These losses were different relative to women who used neither agent: lumbar spine -3.35% (95% CI −5.13%, −1.56%, p = 0.001), total hip −2.24% (95% CI −3.87%, −0.60%, p = 0.009), and femoral neck −1.71% (95% CI −3.73%, 0.31%, p = 0.102). Conclusion: We observed a trend for women with concurrent DMPA and FTC/TDF PrEP use to have 1–3% lower BMD than unexposed women after 12 months.