Background: Nigeria has a high HIV burden with over 3,500,000 infected and more than 200,000 deaths annually. Since 2004, international donor agencies and implementing partners managed HIV programs in Nigeria. Excellence and Friends Management Care Centre (EFMC) was the first local organization to be funded to provide comprehensive HIV services in Nigeria. Aim: To document the need, processes and products of five years of indigenous HIV programming in Nigeria. Materials and Methods: PEPFAR funded EFMC from 2011 to provide comprehensive HIV services in Nasarawa State and Abuja, the Federal Capital Territory (FCT). EFMC engaged staff, assessed and activated sites, trained and empowered healthcare workers, provided consumables, enrolled clients and provided preventive, treatment and support services. EFMC also strengthened healthcare systems and refurbished and equipped facilities for integrated HIV services. Results: EFMC decentralized, commonized and integrated HIV services in over 120 service delivery points with an average cost per target of US$ 273.12. We tested 623,148 people for HIV. The positivity rate was 3.3% (annual range 1.9–4.5%). We placed 10,150 on Highly Active Antiretroviral Therapy. In addition, we tested 164,746 pregnant women for HIV with 5,442 (3.3%) positive and provided 4,189 (77.0%) positive pregnant women with ARV prophylaxis. More than 500 healthcare workers in HIV program management. Conclusions: EFMC’s “commonization” model is cost-effective and efficient. Progressively funding local partners will ensure sustainability of HIV programs. Using program results as national figures will save cost from periodic sentinel studies. Government should support local NGOs to control the HIV epidemic in Nigeria.