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Background Nigeria has one of the largest Human Immunodeficiency Virus (HIV) epidemics in the world. Addressing the epidemic of HIV in such a high-burden country has necessitated responses of a multidimensional nature. Historically, community-based organizations (CBOs) have played an essential role in targeting key populations (eg. men who have sex with men, sex workers) that are particularly burdened by HIV. CBOs are an essential part of the provision of health services in sub-Saharan Africa, but very little is known about the management practices of CBOs that provide HIV prevention interventions. Methods We interviewed 31 CBO staff members and other key stakeholders in January 2017 about management practices in CBOs. Management was conceptualized under the classical management process perspective; these four management phases—planning, organizing, leading, and evaluating—guided the interview process and code development. Data analysis was conducted thematically using Atlas.ti software. The protocol was approved by the ethics committees of the National Institute of Public Health of Mexico (INSP), the National Agency for the Control of AIDS in Nigeria (NACA), and the Nigerian Institute for Medical Research (NIMR). Results We found that CBOs implement variable management practices that can either hinder or facilitate the efficient provision of HIV prevention services. Long-standing CBOs had relatively strong organizational infrastructure and capacity that positively influenced service planning. In contrast, fledgling CBOs were deficient of organizational infrastructure and lacked program planning capacity. The delivery of HIV services can become more efficient if management practices are taken into account. Conclusions The delivery of HIV services by CBOs in Nigeria was largely influenced by inherent issues related to skills, organizational structure, talent retention, and sanction application. These, in turn, affected management practices such as planning, organizing, leading, and evaluating. This study shows that KP-led CBOs are evolving and have strong potentials and capacity for growth, and can become more efficient and effective if attention is paid to issues such as hierarchy, staff recruitment, and talent retention.