The Truth, Peaceful Coexistence, and Non-Repetition Commission (CEV) is one of the transitional justice mechanisms contained in the peace agreement signed between the Colombian government and the Revolutionary Armed Forces of Colombia (FARC) guerrilla in 2016. The CEV mainstreams gender and ethnic differential approaches and is also the first to actively deploy intersectionality as a framework to approach violence committed against women of ethnic groups. The article draws on a decolonial and intercultural perspective to analyze the challenges that the CEV faces to make visible Indigenous women’s experiences and agencies during the armed conflict. Based on participatory research conducted with Arhuaco women of the Sierra Nevada de Santa Marta to produce a report to the CEV, the article shows the methodological gaps that exist between Arhuaco women’s approaches to memory and the Truth Commission’s methodological framework. The article also argues that the Commission’s strategy to confront political dynamics within Indigenous communities that marginalize women’s processes further deepens these gaps and contributes to invisibilize their voices in this scenario.