Despite increasing engagement of patients and other stakeholders in the research process, little is known about its impact, particularly over the long term. In this qualitative descriptive study, we sought to explore how stakeholders who participated in a chronic kidney disease (CKD) research prioritization exercise two years earlier viewed their engagement experience and the research priorities. Through thematic analysis of interviews with 23 participants across stakeholder groups (patients, caregivers, healthcare providers and policymakers) and levels of engagement (steering committee, workshop and wiki), we identified four themes related to perceived engagement and three themes related to views on the CKD research priorities and prioritization process. Our findings highlight important considerations to support meaningful engagement in research prioritization, including roles and expertise, representation, and communication, and characterize ways in which individual priorities can change over time. Findings may contribute toward optimizing the design and conduct of future research engaging patients as stakeholders.