Transitional justice systems generally aim to achieve two goals. One is to bring the perpetrators of past atrocities to justice to ensure that they do not go unpunished, which involves the State fulfilling its duty to investigate, prosecute and punish serious human rights violations and breaches of international humanitarian law (IHL). The other is to bring about reconciliation to heal a divided society and achieve peace and stability. This normally requires the adoption of measures of clemency, such as granting amnesty, so that those who took part in the country's violent past can return to civilian life. The use of IHL is relevant in attaining both these goals because its complex nature means that it provides the legal basis for their implementation. However, this very complexity can mean that there are contradictions or complementarities between its characteristics. This article looks at the case of the Special Jurisdiction for Peace (JEP) in Colombia, showing how this transitional jurisdiction has used IHL as a legal basis both for investigating, prosecuting and punishing serious violations committed during the Colombian armed conflict and for granting amnesty to those who took part in the hostilities. These different uses by the JEP demonstrate that IHL is a flexible tool that can facilitate the process of delivering both justice and peace after a conflict has ended.