Humanitarian supply chains (HSCs) contribute significantly to achieving effective and rapid responses to natural and man-made disasters. Though humanitarian organizations have during the last decades made considerable efforts to improve the response to crises in terms of effectiveness and efficiency, HSCs are still faced with so many challenges, one of which is the incorporation of sustainability dimensions (economic, social and environmental) in the management of their supply chains. In the literature, some authors have highlighted that the planning and achievement of sustainability performance objectives in humanitarian operations is hindered by the lack of decision support systems (DSS). Therefore, this paper proposes a multi-objective Master Planning DSS for managing sustainable HSCs. This Master Planning DSS includes: (1) the definition of a set of metrics for measuring the performance of a sustainable HSC; (2) an algorithm to solve the multi-objective problem; and (3) a Master Planning mathematical model to support the tactical planning of the sustainable HSC. Using the information gathered from field research and the literature, an illustrative numerical example is presented to demonstrate the implementation and utility of the proposed DSS. The results show that the order in which the three sustainability dimensions (economic, social and environmental) are prioritized has some impact on the performance measures. Therefore, it is important to fix a tolerance that would enable to obtain an acceptable balance (trade-off) between the three sustainability objectives, in line with the prioritization choice of the decision maker. The paper can be accessed via the following link: https://rdcu.be/NUkB as a part of Springer’s SharedIt Initiative.