Patient engagement in healthcare is increasingly discussed in the literature, and initiatives engaging patients in quality improvement activities, organizational design, governance, and research are becoming more and more common and have even become mandatory for certain health institutions. Here we discuss a number of ethical challenges raised by this engagement from patients from the perspectives of research, organizational/quality improvement practices, and patient experiences, while offering preliminary recommendations as to how to address them. We identified three broad categories of ethical issues that intersect between the different types of patient engagement: (1) establishing a shared vision about goals of patient engagement and respective roles; (2) the process and method of engaging with patients; and (3) practical aspects of patient engagement. To explain these issues, we build from our personal, professional, and academic experiences, as well as traditions such as pragmatism and hermeneutics that stress the importance of participation, empowerment, and engagement.  Patient engagement can be highly valuable at numerous levels, but particular attention should be paid to the process of engaging with patients and related ethical issues. Some lessons from the literature on the ethics of participatory research can be translated to organizational and quality improvement practices.