Health technology assessment (HTA) is increasingly used around the globe to inform resource allocation decisions. Furthermore, the importance of using explicit and transparent criteria for coverage decision making in line with health system values has been acknowledged. However, the values of a health system are often not explicitly taken into account in the HTA process. This situation influences the allocation of scarce resources and could lead to a discord between the HTA outcome and the values of the health system. We describe how evidence-informed deliberative processes (EDPs) can help to improve this situation. EDPs are integrating two theoretical frameworks; multi-criteria decision-analysis and accountability for reasonableness. Through the use of EDPs, HTA agencies can ensure that health system values are more explicitly and consistently taken into account in the HTA process, enhancing the legitimacy of coverage decisions.