Prison staff face situations with conflicting interests and values. To strengthen craftsmanship Dutch prison staff reflected upon personal moral dilemmas during Moral Case Deliberation (MCD) sessions. This research aims to gain systematic insight into themes and moral dilemmas Dutch prison staff encounter. Evaluation-forms of 171 MCD-sessions were collected (N = 1065 MCD-participants, N = 171 MCD-facilitators) from 22 teams of different professional disciplines at 3 locations. Our qualitative thematic content analysis included 154 moral dilemmas. We noted the organizational level and professional disciplines the moral dilemmas related to, and how dilemmas were formulated. All professional disciplines within prison work show to encounter a wide range of moral dilemmas, which emerge in and between all organizational levels. “Security” and “cooperation” were frequently mentioned themes, while dilemmas relating to the rehabilitation of prisoners were underrepresented. Some formulations of moral dilemmas were based on frustrations toward colleagues or the organization, expressed “powerlessness” to change practice, or contained normative arguments instead of an open formulation. These insights call for structural facilitation of methods for prison staff to deal with moral dilemmas. Ethics Support Services (ESS), such as MCD-sessions, can be used to further strengthen the moral craftsmanship of prison staff.