There is an increased focus on fostering integrity in research by through creating an open culture where research integrity dilemmas can be discussed. We describe a pilot intervention study that used Moral Case Deliberation (MCD), a method that originated in clinical ethics support, to discuss research integrity dilemmas with researchers. Our research question was: can moral case deliberation in research groups help to navigate research integrity dilemmas? We performed 10 MCDs with 19 researchers who worked in three different research groups from three different disciplinary fields at a university in the Netherlands. We analyzed the dilemmas and values discussed, sent out a survey questionnaire to assess self-perceived moral competencies, and conducted in-depth interviews. We found research integrity dilemmas pertained to authorship disputes, supervision of junior co-workers, and questionable handling of data. Participants perceived the majority of moral competencies to a higher degree during the MCD when compared to perceiving them in daily practice afterward. Interviewees told us that they felt most comfortable discussing dilemmas among peers with whom they were not closely affiliated. We conclude that MCD sessions could be relevant in navigating research integrity dilemmas, but that revisions to ensure commitment and safety are required.