Background Drug policy is prone to build on rationales based on different moralities rather than evidence. Less is known about how moralities influence drug policy implementation in practice. The aim was to analyze expressions of moralities among local policy-makers, professionals, and drug users in the context of the Stockholm needle and syringe exchange program (NSP). Methods Using political documentation from Stockholm (2003–2016), focus group (12 NSP staff), and 32 drug user interviews, moralities concerning drug policy and harm reduction were analyzed based on moral foundations theory and boundary work. Results Three main moral dilemmas were identified concerning the subjects, aims, and orientation of drug policy: whether drug users are worthy of inclusion to society; if the general public should be prioritized or the health of drug users, and the orientation of practices as based on control or autonomy. Policy debate was driven by virtues such as purity and authority, whereas staff and drug users valued care, fairness and liberty. Conclusions The prohibitionist and abstinence-oriented Swedish drug policy has created social boundaries on the practice-level. Hence, users’ perspectives, and those who care about them, should be extensively involved in political discussions to foster a more moral and humane drug policy.