The aim of the study was to identify the proportion of female sex workers, men who have sex with men, and people who inject drugs who had accessed HIV prevention services at public health facilities and peer-led facilities, their level of satisfaction with these services, and perceived barriers and challenges to accessing HIV services from public and peer-led HIV prevention service providers.A mixed-method approach was used to collect data from key populations in the four states in Nigeria. Quantitative data collected included level of satisfaction with and barriers to use of public and peer-led facilities. In-depth interviews and focus-group discussions were conducted to explore reasons for satisfaction with and barriers to use of services. Descriptive and bivariate analyses were was conducted for quantitative data. Qualitative data were summaried, emerging themes identified, described and quotes reflecting the themes corresponding to interview questions highlighted.Nine hundred sixty-seven persons responded to questions on the use of public health or/and peer-led facilities. Two hundred thirty-eight (49.4%) respondents had received HIV and sexual and reproductive health services through public health facilities, and 236 (48.7%) had received the services through peer-led facilities. Significantly more respondents were satisfied with the quality of services provided by peer-led organisations than with public health facilities with respect to service providers listening to respondent's problems and concerns (p = 0.007),privacy and confidentiality (p = 0.04) and respect of rights of service recipients (p = 0.04). Significantly more respondents using peer-led organisations than those using public health facilities identified no barriers to service access (p = 0.003). More respondents using public health facilities than peer-led facilities identified cost of services (p = 0.01), confidentiality (p = 0.002), waiting time (p < 0.01) and staff attitude (p = 0.001) as barriers to service access. Thee was no difference in the proportion of respondents willing to discontinue their use of either facilities (p = 0.08). Qualitative data revealed that concerns with access of services at the public health facility were due mainly to stigma and the effects of the same-sex prohibition law.Key populations were more satisfied receiving HIV prevention services at peer-led organisations than at public health facilities.