Background The Dialogue Model for research agenda‐setting, involving multiple stakeholders including patients, was developed and validated in the Netherlands. However, there is little insight into whether and how patient involvement is sustained during the programming and implementation of research agendas. Aim To understand how the Dialogue Model can be optimised by focusing on programming and implementation, in order to stimulate the inclusion of (the perspectives of) patients in research. Methods A responsive evaluation of the programming and implementation phases of nine agenda‐setting projects that had used the Dialogue Model for agenda‐setting was conducted. Fifty‐four semi‐structured interviews were held with different stakeholders (patients, researchers, funding agencies). Three focus groups with patients, funding agencies and researchers (16 participants) were organized to validate the findings. Results Patient involvement in programming and implementation of the research agendas was limited. This was partly related to poor programming and implementation, partly to pitfalls in earlier phases of the agenda‐setting. Optimization of the Dialogue Model is possible by attending to the nature of the agenda and its intended use in earlier phases. Attention should also be given to the ambassadors and intended users of agenda topics. Support is needed during programming and implementation to organize patient involvement and adapt organizational structures like review procedures. In all phases the attitude to patient involvement, stakeholder participation, especially of researchers, and formal and informal relationships between parties need to be addressed to build a strong relationship with a shared goal. Conclusion Patient involvement in agenda‐setting is not automatically followed by patient involvement in programming and implementation. More attention should be paid, in earlier stages, to the attitude and engagement of researchers and funding agencies.