We examined how the perception that separatist groups threaten the majority’s moral identity impacts the latter group’s support for reconciliation in separatist conflict. Two studies were conducted in Indonesia, where separatist conflict is rife. Javanese students (representing the nonseparatist majority) responded surveys regarding separatist conflicts in Aceh (Study 1, N = 679) or West Papua (Study 2, N = 500). As expected, perceived threat to the majority’s moral identity increased this particular group’s reconciliatory attitudes (Study 1), emotions, and behaviours (Study 2), through increased compensatory needs for social acceptance and restoration of moral image. These findings underline the importance of moral identity dynamics in separatist conflict. Moreover, they reveal that the majority, despite its dominant position, can experience morality threat from separatist groups which can foster positive attitudes towards the reconciliation process.