A set of survey questionnaires produced for a longitudinal behavioural-biological cohort survey of female sex workers (FSWs) in Nairobi, Kenya. Data was collected at three time-points – the Baseline survey was performed between June-December 2019, the Midline survey between January-March 2020 (pre-COVID-19), and the Endline survey was performed between June 2020-March 2021 (during the COVID-19 pandemic).