Negotiations are part of systemic interventions. Because moral frameworks affect goal setting and decision‐making processes in negotiation, they can have an important effect in systemic interventions. In this paper, we use critical systems thinking to improve our understanding of the structure of moral frameworks and judgments in negotiation. We explore several moral frameworks that are applied in negotiation, and we demonstrate how boundary critique can be employed to understand and deal more reflexively and holistically with moral judgments that are part of negotiations in systemic interventions. By adopting a critical perspective of our assumptions and rationality in negotiation practice, we attempt to show how to open negotiations that are part of systemic interventions to more reflexive and informed possibilities. This can help us to avoid implementing changes in a systemic intervention that promote moral perspectives, which are not based on a holistic and reflexive exploration of the stakeholders' moral frameworks. © 2018 John Wiley & Sons, Ltd.