Background: Female sex workers (FSWs) are at increased risk of HIV and STIs compared to women in the general population, and frequently experience violence in their working and domestic lives from a variety of perpetrators, which can enhance this risk. While progress has been made in addressing violence by police and clients, little work has been done to understand and prevent violence by intimate partners (IPs) among FSW populations. Methods: Samvedana Plus is a multi-level intervention programme that works with FSWs, their IPs, the sex worker community, and the general population, and aims to reduce violence and increase consistent condom use within these 'intimate' relationships. The programme involves shifting norms around the acceptability of beating as a form of discipline, challenging gender roles that give men authority over women, and working with men and women to encourage new relationship models based on gender equity and respect. The programme will aim to cover 800 FSWs and their IPs living in 47 villages in Bagalkot district, northern Karnataka. The study is designed to assess two primary outcomes: the proportion of FSWs who report: (i) physical or sexual partner violence; and (ii) consistent condom use in their intimate relationship, within the past 6 months. The evaluation will employ a cluster-randomised controlled trial design, with 50 % of the village clusters (n = 24) randomly selected to receive the intervention for the first 24 months and the remaining 50 % (n = 23) receiving the intervention thereafter. Statisticians will be blinded to treatment arm allocation. The evaluation will use an adjusted, cluster-level intention to treat analysis, comparing outcomes in intervention and control villages at midline (12 months) and endline (24 months). The evaluation design will involve quantitative and qualitative assessments with (i) all FSWs who report an IP (ii) IPs; and process/implementation monitoring. Baseline data collection was completed in April 2015, and endline data collection is anticipated in May 2017. Conclusions: This is an innovative intervention programme that aims to address violence by IPs as part of HIV prevention programming with FSWs. Reducing violence is expected to reduce vulnerability to HIV acquisition, and help women to work and live without fear of violence. Trial registration: Clinical Trials NCT02807259 Jun 24 2016 (retrospectively registered).