Globally, HIV/AIDS is the leading cause of morbidity and mortality among adolescents; sub-Saharan Africa contributes more than two-thirds of all HIV-related adolescent deaths. In Kenya, HIV incidence remains high among youth (15–24 years), with women disproportionately affected. Morbidity and mortality are compounded by a high rate of early and unwanted pregnancies. Existing prevention efforts to reduce youth vulnerabilities overwhelmingly focus on HIV alone, with limited efforts made to address concurrent factors that increase vulnerability of adolescent girls and young women (AGYW) to HIV infection and unplanned pregnancies. Jilinde, is a Bill and Melinda Gates Foundation funded large-scale project that supports the provision of pre-exposure prophylaxis (PrEP) in Kenya. This manuscript presents a protocol for a study that seeks to evaluate the effectiveness of a comprehensive package of user-centered interventions to optimize uptake of HIV and pregnancy prevention services among AGYW in four Kenyan counties.