Abstract Provider payment mechanisms (PPMs) are important to the universal health coverage (UHC) agenda as they can influence healthcare provider behaviour and create incentives for health service delivery, quality and efficiency. Therefore, when designing PPMs, it is important to consider providers’ preferences for PPM characteristics. We set out to uncover senior health facility managers’ preferences for the attributes of a capitation payment mechanism in Kenya. We use a discrete choice experiment and focus on four capitation attributes, namely, payment schedule, timeliness of payments, capitation rate per individual per year and services to be paid by the capitation rate. Using a Bayesian efficient experimental design, choice data were collected from 233 senior health facility managers across 98 health facilities in seven Kenyan counties. Panel mixed multinomial logit and latent class models were used in the analysis. We found that capitation arrangements with frequent payment schedules, timelier disbursements, higher payment rates per individual per year and those that paid for a limited set of health services were preferred. The capitation rate per individual per year was the most important attribute. Respondents were willing to accept an increase in the capitation rate to compensate for bundling a broader set of health services under the capitation payment. In addition, we found preference heterogeneity across respondents and latent classes. In conclusion, these attributes can be used as potential targets for interventions aimed at configuring capitation to achieve UHC.