His research focuses on multidisciplinary studies of epidemiology and prevention of HIV and other STIs, implementation science, and antiretroviral pre-exposure prophylaxis (PrEP) pharmacology in African populations, particularly among young women. Over the past decade, he has led or collaborated on pivotal HIV prevention studies involving >30,000 HIV at-risk participants that have advanced PrEP implementation and HIV prevention for populations in Africa and globaly. He led key analyses to quantify and interpret the risk and safety of oral TDF-based PrEP in African populations, demonstrating no substantial sexual risk compensation and limited kidney toxicity. He led the only pharmacokinetics study of infant exposure to TDF/FTC PrEP via breastmilk demonstrating limited breastmilk excretion and low infant absorption. Dr. Mugwanya is the PI of an NIH-funded stepped-wedge cluster randomized trial aiming to catalyze integration of PrEP and comprehensive HIV prevention services for women accessing Kenyan family planning clinics.