Abstract Background Efforts to engage patients as partners in health research have grown and thereby the need for feedback and evaluation. In this pilot evaluation study, we aimed to 1) evaluate patient engagement in health research projects in Newfoundland and Labrador, Canada, and 2) learn more about how to best monitor and evaluate patient engagement. This paper presents the results of our participatory evaluation study and the lessons learned. The evaluation of the projects was driven by questions patients wanted answered. Methods We conducted a formative evaluation of patient engagement in health research projects. Projects spanned a variety of topics, target groups, research designs and methods of patient engagement. Participants included principal investigators (n = 6) and their patient partners (n = 14). Furthermore, graduate students (n = 13) working on their own research projects participated. Participants completed an online survey with closed and open-ended questions about their patient engagement efforts, experiences and preliminary outcomes. Patients were involved as co-investigators in the entire evaluation study. We used qualitative methods to evaluate our participatory process. Results The evaluation study results show that most patients and researchers felt prepared and worked together in various phases of the research process. Both groups felt that the insights and comments of patients influenced research decisions. They believed that patient engagement improved the quality and uptake of research. Students felt less prepared and were less satisfied with their patient engagement experience compared to researchers and their patient partners. Involvement of patient co-investigators in this evaluation resulted in learnings, transparency, validation of findings and increased applicability. Challenges were to select evaluation questions relevant to all stakeholders and to adapt evaluation tools to local needs. Conclusions Our findings show that researchers, patient partners and students value patient engagement in health research. Capacity building at the supervisor level in academic institutions is needed to better support students. Sufficient time is also needed to permit observable outcomes. Participatory evaluation may increase the relevance and usefulness of information, but it also raises issues such as who defines and designs the content of evaluation tools. A co-creation process is required to develop appropriate monitoring and evaluation strategies.