BACKGROUND: Female sex workers (FSW) in sub-Saharan Africa are disproportionately affected by HIV and are critical to engage in HIV prevention, testing and care services. We describe the design of our evaluation of the 'AMETHIST' intervention, nested within a nationally-scaled programme for FSW in Zimbabwe. We hypothesise that the implementation of this intervention will result in a reduction in the risk of HIV transmission within sex work. METHODS: The AMETHIST intervention (Adapted Microplanning to Eliminate Transmission of HIV in Sex Transactions) is a risk-differentiated intervention for FSW, centred around the implementation of microplanning and self-help groups. It is designed to support uptake of, and adherence to, HIV prevention, testing and treatment behaviours among FSW. Twenty-two towns in Zimbabwe were randomised to receive either the Sisters programme (usual care) or the Sisters programme plus AMETHIST. The composite primary outcome is defined as the proportion of all FSW who are at risk of either HIV acquisition (HIV-negative and not fully protected by prevention interventions) or of HIV transmission (HIV-positive, not virally suppressed and not practicing consistent condom use). The outcome will be assessed after 2 years of intervention delivery in a respondent-driven sampling survey (total n = 4400; n = 200 FSW recruited at each site). Primary analysis will use the 'RDS-II' method to estimate cluster summaries and will adapt Hayes and Moulton's '2-step' method produce adjusted effect estimates. An in-depth process evaluation guided by our project trajectory will be undertaken. DISCUSSION: Innovative pragmatic trials are needed to generate evidence on effectiveness of combination interventions in HIV prevention and treatment in different contexts. We describe the design and analysis of such a study. TRIAL REGISTRATION: Pan African Clinical Trials Registry PACTR202007818077777 . Registered on 2 July 2020.